This Snakemake pipeline implements the GATK best-practices workflow

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dna-seq-gatk-variant-calling
dna-seq-gatk-variant-calling
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This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants.

Usage

The usage of this workflow is described in the Snakemake Workflow Catalog .

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).

Code Snippets

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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


import os

from snakemake.shell import shell

known = snakemake.input.get("known", "")
if known:
    known = "--dbsnp " + known

extra = snakemake.params.get("extra", "")
java_opts = snakemake.params.get("java_opts", "")
bams = snakemake.input.bam
if isinstance(bams, str):
    bams = [bams]
bams = list(map("-I {}".format, bams))

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
    "gatk --java-options '{java_opts}' HaplotypeCaller {extra} "
    "-R {snakemake.input.ref} {bams} "
    "-ERC GVCF "
    "-O {snakemake.output.gvcf} {known} {log}"
)
Python Snakemake gatk From line 1 of haplotypecaller/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
java_opts = snakemake.params.get("java_opts", "")

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
    "gatk --java-options '{java_opts}' SelectVariants -R {snakemake.input.ref} -V {snakemake.input.vcf} "
    "{extra} -O {snakemake.output.vcf} {log}"
)
Python Snakemake gatk From line 1 of selectvariants/wrapper.py 
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__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2016, Patrik Smeds"
__email__ = "[email protected]"
__license__ = "MIT"

from os import path

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

# Check inputs/arguments.
if len(snakemake.input) == 0:
    raise ValueError("A reference genome has to be provided!")
elif len(snakemake.input) > 1:
    raise ValueError("Only one reference genome can be inputed!")

# Prefix that should be used for the database
prefix = snakemake.params.get("prefix", "")

if len(prefix) > 0:
    prefix = "-p " + prefix

# Contrunction algorithm that will be used to build the database, default is bwtsw
construction_algorithm = snakemake.params.get("algorithm", "")

if len(construction_algorithm) != 0:
    construction_algorithm = "-a " + construction_algorithm

shell(
    "bwa index" " {prefix}" " {construction_algorithm}" " {snakemake.input[0]}" " {log}"
)
Python Snakemake BWA From line 1 of index/wrapper.py 
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__author__ = "Johannes Köster, Julian de Ruiter"
__copyright__ = "Copyright 2016, Johannes Köster and Julian de Ruiter"
__email__ = "[email protected], [email protected]"
__license__ = "MIT"


from os import path

from snakemake.shell import shell


# Extract arguments.
extra = snakemake.params.get("extra", "")

sort = snakemake.params.get("sort", "none")
sort_order = snakemake.params.get("sort_order", "coordinate")
sort_extra = snakemake.params.get("sort_extra", "")

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

# Check inputs/arguments.
if not isinstance(snakemake.input.reads, str) and len(snakemake.input.reads) not in {
    1,
    2,
}:
    raise ValueError("input must have 1 (single-end) or " "2 (paired-end) elements")

if sort_order not in {"coordinate", "queryname"}:
    raise ValueError("Unexpected value for sort_order ({})".format(sort_order))

# Determine which pipe command to use for converting to bam or sorting.
if sort == "none":

    # Simply convert to bam using samtools view.
    pipe_cmd = "samtools view -Sbh -o {snakemake.output[0]} -"

elif sort == "samtools":

    # Sort alignments using samtools sort.
    pipe_cmd = "samtools sort {sort_extra} -o {snakemake.output[0]} -"

    # Add name flag if needed.
    if sort_order == "queryname":
        sort_extra += " -n"

    prefix = path.splitext(snakemake.output[0])[0]
    sort_extra += " -T " + prefix + ".tmp"

elif sort == "picard":

    # Sort alignments using picard SortSam.
    pipe_cmd = (
        "picard SortSam {sort_extra} INPUT=/dev/stdin"
        " OUTPUT={snakemake.output[0]} SORT_ORDER={sort_order}"
    )

else:
    raise ValueError("Unexpected value for params.sort ({})".format(sort))

shell(
    "(bwa mem"
    " -t {snakemake.threads}"
    " {extra}"
    " {snakemake.params.index}"
    " {snakemake.input.reads}"
    " | " + pipe_cmd + ") {log}"
)
Python Snakemake SAMtools Picard From line 1 of mem/wrapper.py 
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__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "[email protected]"
__license__ = "MIT"


from os import path
import re
from tempfile import TemporaryDirectory

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=True, stderr=True)


def basename_without_ext(file_path):
    """Returns basename of file path, without the file extension."""

    base = path.basename(file_path)
    # Remove file extension(s) (similar to the internal fastqc approach)
    base = re.sub("\\.gz$", "", base)
    base = re.sub("\\.bz2$", "", base)
    base = re.sub("\\.txt$", "", base)
    base = re.sub("\\.fastq$", "", base)
    base = re.sub("\\.fq$", "", base)
    base = re.sub("\\.sam$", "", base)
    base = re.sub("\\.bam$", "", base)

    return base


# Run fastqc, since there can be race conditions if multiple jobs
# use the same fastqc dir, we create a temp dir.
with TemporaryDirectory() as tempdir:
    shell(
        "fastqc {snakemake.params} -t {snakemake.threads} "
        "--outdir {tempdir:q} {snakemake.input[0]:q}"
        " {log}"
    )

    # Move outputs into proper position.
    output_base = basename_without_ext(snakemake.input[0])
    html_path = path.join(tempdir, output_base + "_fastqc.html")
    zip_path = path.join(tempdir, output_base + "_fastqc.zip")

    if snakemake.output.html != html_path:
        shell("mv {html_path:q} {snakemake.output.html:q}")

    if snakemake.output.zip != zip_path:
        shell("mv {zip_path:q} {snakemake.output.zip:q}")
Python Snakemake FastQC From line 3 of fastqc/wrapper.py 
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__author__ = "Christopher Schröder"
__copyright__ = "Copyright 2020, Christopher Schröder"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
shell(
    "gatk --java-options '{java_opts}' ApplyBQSR {extra} "
    "-R {snakemake.input.ref} -I {snakemake.input.bam} "
    "--bqsr-recal-file {snakemake.input.recal_table} "
    "-O {snakemake.output.bam} {log}"
)
Python Snakemake gatk snakemake-wrapper-utils From line 1 of applybqsr/wrapper.py 
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__author__ = "Christopher Schröder"
__copyright__ = "Copyright 2020, Christopher Schröder"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
known = snakemake.input.get("known", "")
if known:
    if isinstance(known, str):
        known = [known]
    known = list(map("--known-sites {}".format, known))

shell(
    "gatk --java-options '{java_opts}' BaseRecalibrator {extra} "
    "-R {snakemake.input.ref} -I {snakemake.input.bam} "
    "-O {snakemake.output.recal_table} {known} {log}"
)
Python Snakemake gatk snakemake-wrapper-utils From line 1 of baserecalibrator/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


import os

from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

gvcfs = list(map("-V {}".format, snakemake.input.gvcfs))

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
    "gatk --java-options '{java_opts}' CombineGVCFs {extra} "
    "{gvcfs} "
    "-R {snakemake.input.ref} "
    "-O {snakemake.output.gvcf} {log}"
)
Python Snakemake gatk snakemake-wrapper-utils From line 1 of combinegvcfs/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


import os

from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
interval_file = snakemake.input.get("interval_file", "")
if interval_file:
    interval_file = "-L {}".format(interval_file)
dbsnp = snakemake.input.get("known", "")
if dbsnp:
    dbsnp = "-D {}".format(dbsnp)

# Allow for either an input gvcf or GenomicsDB
gvcf = snakemake.input.get("gvcf", "")
genomicsdb = snakemake.input.get("genomicsdb", "")
if gvcf:
    if genomicsdb:
        raise Exception("Only input.gvcf or input.genomicsdb expected, got both.")
    input_string = gvcf
else:
    if genomicsdb:
        input_string = "gendb://{}".format(genomicsdb)
    else:
        raise Exception("Expected input.gvcf or input.genomicsdb.")
tmp_dir = snakemake.params.get("tmp_dir", "")
if tmp_dir:
    tmp_dir = "--tmp-dir={}".format(tmp_dir)

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
    "gatk --java-options '{java_opts}' GenotypeGVCFs {extra} "
    "-V {input_string} "
    "-R {snakemake.input.ref} "
    "{dbsnp} "
    "{interval_file} "
    "{tmp_dir} "
    "-O {snakemake.output.vcf} {log}"
)
Python Snakemake gatk snakemake-wrapper-utils From line 1 of genotypegvcfs/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

filters = [
    "--filter-name {} --filter-expression '{}'".format(name, expr.replace("'", "\\'"))
    for name, expr in snakemake.params.filters.items()
]

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
    "gatk --java-options '{java_opts}' VariantFiltration -R {snakemake.input.ref} -V {snakemake.input.vcf} "
    "{extra} {filters} -O {snakemake.output.vcf} {log}"
)
Python Snakemake gatk snakemake-wrapper-utils From line 1 of variantfiltration/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


import os

from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)


def fmt_res(resname, resparams):
    fmt_bool = lambda b: str(b).lower()
    try:
        f = snakemake.input.get(resname)
    except KeyError:
        raise RuntimeError(
            "There must be a named input file for every resource (missing: {})".format(
                resname
            )
        )
    return "{},known={},training={},truth={},prior={} {}".format(
        resname,
        fmt_bool(resparams["known"]),
        fmt_bool(resparams["training"]),
        fmt_bool(resparams["truth"]),
        resparams["prior"],
        f,
    )


resources = [
    "--resource:{}".format(fmt_res(resname, resparams))
    for resname, resparams in snakemake.params["resources"].items()
]
annotation = list(map("-an {}".format, snakemake.params.annotation))
tranches = ""
if snakemake.output.tranches:
    tranches = "--tranches-file " + snakemake.output.tranches

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
    "gatk --java-options '{java_opts}' VariantRecalibrator {extra} {resources} "
    "-R {snakemake.input.ref} -V {snakemake.input.vcf} "
    "-mode {snakemake.params.mode} "
    "--output {snakemake.output.vcf} "
    "{tranches} {annotation} {log}"
)
Python Snakemake gatk snakemake-wrapper-utils From line 1 of variantrecalibrator/wrapper.py 
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__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "[email protected]"
__license__ = "MIT"


from os import path

from snakemake.shell import shell


input_dirs = set(path.dirname(fp) for fp in snakemake.input)
output_dir = path.dirname(snakemake.output[0])
output_name = path.basename(snakemake.output[0])
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
    "multiqc"
    " {snakemake.params}"
    " --force"
    " -o {output_dir}"
    " -n {output_name}"
    " {input_dirs}"
    " {log}"
)
Python Snakemake MultiQC From line 3 of multiqc/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
bams = snakemake.input
if isinstance(bams, str):
    bams = [bams]
bams = list(map("INPUT={}".format, bams))

shell(
    "picard MarkDuplicates "  # Tool and its subcommand
    "{java_opts} "  # Automatic java option
    "{extra} "  # User defined parmeters
    "{bams} "  # Input bam(s)
    "OUTPUT={snakemake.output.bam} "  # Output bam
    "METRICS_FILE={snakemake.output.metrics} "  # Output metrics
    "{log}"  # Logging
)
Python Snakemake Picard snakemake-wrapper-utils From line 1 of markduplicates/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


inputs = " ".join("INPUT={}".format(f) for f in snakemake.input.vcfs)
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

shell(
    "picard"
    " MergeVcfs"
    " {java_opts}"
    " {extra}"
    " {inputs}"
    " OUTPUT={snakemake.output[0]}"
    " {log}"
)
Python Snakemake Picard snakemake-wrapper-utils From line 3 of mergevcfs/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2019, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"

import subprocess as sp
import sys
from itertools import product
from snakemake.shell import shell

species = snakemake.params.species.lower()
release = int(snakemake.params.release)
build = snakemake.params.build

branch = ""
if release >= 81 and build == "GRCh37":
    # use the special grch37 branch for new releases
    branch = "grch37/"

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

spec = ("{build}" if int(release) > 75 else "{build}.{release}").format(
    build=build, release=release
)

suffixes = ""
datatype = snakemake.params.get("datatype", "")
chromosome = snakemake.params.get("chromosome", "")
if datatype == "dna":
    if chromosome:
        suffixes = ["dna.chromosome.{}.fa.gz".format(chromosome)]
    else:
        suffixes = ["dna.primary_assembly.fa.gz", "dna.toplevel.fa.gz"]
elif datatype == "cdna":
    suffixes = ["cdna.all.fa.gz"]
elif datatype == "cds":
    suffixes = ["cds.all.fa.gz"]
elif datatype == "ncrna":
    suffixes = ["ncrna.fa.gz"]
elif datatype == "pep":
    suffixes = ["pep.all.fa.gz"]
else:
    raise ValueError("invalid datatype, must be one of dna, cdna, cds, ncrna, pep")

if chromosome:
    if not datatype == "dna":
        raise ValueError(
            "invalid datatype, to select a single chromosome the datatype must be dna"
        )

success = False
for suffix in suffixes:
    url = "ftp://ftp.ensembl.org/pub/{branch}release-{release}/fasta/{species}/{datatype}/{species_cap}.{spec}.{suffix}".format(
        release=release,
        species=species,
        datatype=datatype,
        spec=spec.format(build=build, release=release),
        suffix=suffix,
        species_cap=species.capitalize(),
        branch=branch,
    )

    try:
        shell("curl -sSf {url} > /dev/null 2> /dev/null")
    except sp.CalledProcessError:
        continue

    shell("(curl -L {url} | gzip -d > {snakemake.output[0]}) {log}")
    success = True
    break

if not success:
    print(
        "Unable to download requested sequence data from Ensembl. "
        "Did you check that this combination of species, build, and release is actually provided?",
        file=sys.stderr,
    )
    exit(1)
Python Snakemake From line 1 of ensembl-sequence/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2019, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"

import tempfile
import subprocess
import sys
import os
from snakemake.shell import shell
from snakemake.exceptions import WorkflowError

species = snakemake.params.species.lower()
release = int(snakemake.params.release)
build = snakemake.params.build
type = snakemake.params.type

if release < 98:
    print("Ensembl releases <98 are unsupported.", file=open(snakemake.log[0], "w"))
    exit(1)

branch = ""
if release >= 81 and build == "GRCh37":
    # use the special grch37 branch for new releases
    branch = "grch37/"

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

if type == "all":
    if species == "homo_sapiens" and release >= 93:
        suffixes = [
            "-chr{}".format(chrom) for chrom in list(range(1, 23)) + ["X", "Y", "MT"]
        ]
    else:
        suffixes = [""]
elif type == "somatic":
    suffixes = ["_somatic"]
elif type == "structural_variations":
    suffixes = ["_structural_variations"]
else:
    raise ValueError(
        "Unsupported type {} (only all, somatic, structural_variations are allowed)".format(
            type
        )
    )

species_filename = species if release >= 91 else species.capitalize()

urls = [
    "ftp://ftp.ensembl.org/pub/{branch}release-{release}/variation/vcf/{species}/{species_filename}{suffix}.{ext}".format(
        release=release,
        species=species,
        suffix=suffix,
        species_filename=species_filename,
        branch=branch,
        ext=ext,
    )
    for suffix in suffixes
    for ext in ["vcf.gz", "vcf.gz.csi"]
]
names = [os.path.basename(url) for url in urls if url.endswith(".gz")]

try:
    gather = "curl {urls}".format(urls=" ".join(map("-O {}".format, urls)))
    workdir = os.getcwd()
    with tempfile.TemporaryDirectory() as tmpdir:
        if snakemake.input.get("fai"):
            shell(
                "(cd {tmpdir}; {gather} && "
                "bcftools concat -Oz --naive {names} > concat.vcf.gz && "
                "bcftools reheader --fai {workdir}/{snakemake.input.fai} concat.vcf.gz "
                "> {workdir}/{snakemake.output}) {log}"
            )
        else:
            shell(
                "(cd {tmpdir}; {gather} && "
                "bcftools concat -Oz --naive {names} "
                "> {workdir}/{snakemake.output}) {log}"
            )
except subprocess.CalledProcessError as e:
    if snakemake.log:
        sys.stderr = open(snakemake.log[0], "a")
    print(
        "Unable to download variation data from Ensembl. "
        "Did you check that this combination of species, build, and release is actually provided? ",
        file=sys.stderr,
    )
    exit(1)
Python Snakemake BCFtools From line 1 of ensembl-variation/wrapper.py 
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__author__ = "Michael Chambers"
__copyright__ = "Copyright 2019, Michael Chambers"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

shell(
    "samtools faidx {snakemake.params} {snakemake.input[0]} > {snakemake.output[0]} {log}"
)
Python Snakemake SAMtools From line 1 of faidx/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
    "samtools index {snakemake.params} {snakemake.input[0]} {snakemake.output[0]} {log}"
)
Python Snakemake SAMtools From line 1 of index/wrapper.py 
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__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell


extra = snakemake.params.get("extra", "")
region = snakemake.params.get("region", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)


shell("samtools stats {extra} {snakemake.input} {region} > {snakemake.output} {log}")
Python Snakemake SAMtools From line 3 of stats/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

shell("tabix {snakemake.params} {snakemake.input[0]} {log}")
Python Snakemake tabix From line 1 of tabix/wrapper.py 
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__author__ = "Johannes Köster, Jorge Langa"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

# Distribute available threads between trimmomatic itself and any potential pigz instances
def distribute_threads(input_files, output_files, available_threads):
    gzipped_input_files = sum(1 for file in input_files if file.endswith(".gz"))
    gzipped_output_files = sum(1 for file in output_files if file.endswith(".gz"))
    potential_threads_per_process = available_threads // (
        1 + gzipped_input_files + gzipped_output_files
    )
    if potential_threads_per_process > 0:
        # decompressing pigz creates at most 4 threads
        pigz_input_threads = (
            min(4, potential_threads_per_process) if gzipped_input_files != 0 else 0
        )
        pigz_output_threads = (
            (available_threads - pigz_input_threads * gzipped_input_files)
            // (1 + gzipped_output_files)
            if gzipped_output_files != 0
            else 0
        )
        trimmomatic_threads = (
            available_threads
            - pigz_input_threads * gzipped_input_files
            - pigz_output_threads * gzipped_output_files
        )
    else:
        # not enough threads for pigz
        pigz_input_threads = 0
        pigz_output_threads = 0
        trimmomatic_threads = available_threads
    return trimmomatic_threads, pigz_input_threads, pigz_output_threads


def compose_input_gz(filename, threads):
    if filename.endswith(".gz") and threads > 0:
        return "<(pigz -p {threads} --decompress --stdout {filename})".format(
            threads=threads, filename=filename
        )
    return filename


def compose_output_gz(filename, threads, compression_level):
    if filename.endswith(".gz") and threads > 0:
        return ">(pigz -p {threads} {compression_level} > {filename})".format(
            threads=threads, compression_level=compression_level, filename=filename
        )
    return filename


extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
compression_level = snakemake.params.get("compression_level", "-5")
trimmer = " ".join(snakemake.params.trimmer)

# Distribute threads
input_files = [snakemake.input.r1, snakemake.input.r2]
output_files = [
    snakemake.output.r1,
    snakemake.output.r1_unpaired,
    snakemake.output.r2,
    snakemake.output.r2_unpaired,
]

trimmomatic_threads, input_threads, output_threads = distribute_threads(
    input_files, output_files, snakemake.threads
)

input_r1, input_r2 = [
    compose_input_gz(filename, input_threads) for filename in input_files
]

output_r1, output_r1_unp, output_r2, output_r2_unp = [
    compose_output_gz(filename, output_threads, compression_level)
    for filename in output_files
]

shell(
    "trimmomatic PE -threads {trimmomatic_threads} {java_opts} {extra} "
    "{input_r1} {input_r2} "
    "{output_r1} {output_r1_unp} "
    "{output_r2} {output_r2_unp} "
    "{trimmer} "
    "{log}"
)
Python Snakemake snakemake-wrapper-utils Trimmomatic From line 12 of pe/wrapper.py 
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__author__ = "Johannes Köster, Jorge Langa"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

# Distribute available threads between trimmomatic itself and any potential pigz instances
def distribute_threads(input_file, output_file, available_threads):
    gzipped_input_files = 1 if input_file.endswith(".gz") else 0
    gzipped_output_files = 1 if output_file.endswith(".gz") else 0
    potential_threads_per_process = available_threads // (
        1 + gzipped_input_files + gzipped_output_files
    )
    if potential_threads_per_process > 0:
        # decompressing pigz creates at most 4 threads
        pigz_input_threads = (
            min(4, potential_threads_per_process) if gzipped_input_files != 0 else 0
        )
        pigz_output_threads = (
            (available_threads - pigz_input_threads * gzipped_input_files)
            // (1 + gzipped_output_files)
            if gzipped_output_files != 0
            else 0
        )
        trimmomatic_threads = (
            available_threads
            - pigz_input_threads * gzipped_input_files
            - pigz_output_threads * gzipped_output_files
        )
    else:
        # not enough threads for pigz
        pigz_input_threads = 0
        pigz_output_threads = 0
        trimmomatic_threads = available_threads
    return trimmomatic_threads, pigz_input_threads, pigz_output_threads


def compose_input_gz(filename, threads):
    if filename.endswith(".gz") and threads > 0:
        return "<(pigz -p {threads} --decompress --stdout {filename})".format(
            threads=threads, filename=filename
        )
    return filename


def compose_output_gz(filename, threads, compression_level):
    if filename.endswith(".gz") and threads > 0:
        return ">(pigz -p {threads} {compression_level} > {filename})".format(
            threads=threads, compression_level=compression_level, filename=filename
        )
    return filename


extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
compression_level = snakemake.params.get("compression_level", "-5")
trimmer = " ".join(snakemake.params.trimmer)

# Distribute threads
trimmomatic_threads, input_threads, output_threads = distribute_threads(
    snakemake.input[0], snakemake.output[0], snakemake.threads
)

# Collect files
input = compose_input_gz(snakemake.input[0], input_threads)
output = compose_output_gz(snakemake.output[0], output_threads, compression_level)

shell(
    "trimmomatic SE -threads {trimmomatic_threads} "
    "{java_opts} {extra} {input} {output} {trimmer} {log}"
)
Python Snakemake snakemake-wrapper-utils Trimmomatic From line 12 of se/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2020, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"

from pathlib import Path
from snakemake.shell import shell


def get_only_child_dir(path):
    children = [child for child in path.iterdir() if child.is_dir()]
    assert (
        len(children) == 1
    ), "Invalid VEP cache directory, only a single entry is allowed, make sure that cache was created with the snakemake VEP cache wrapper"
    return children[0]


extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

fork = "--fork {}".format(snakemake.threads) if snakemake.threads > 1 else ""
stats = snakemake.output.stats
cache = snakemake.input.get("cache", "")
plugins = snakemake.input.plugins

load_plugins = " ".join(map("--plugin {}".format, snakemake.params.plugins))

if snakemake.output.calls.endswith(".vcf.gz"):
    fmt = "z"
elif snakemake.output.calls.endswith(".bcf"):
    fmt = "b"
else:
    fmt = "v"

fasta = snakemake.input.get("fasta", "")
if fasta:
    fasta = "--fasta {}".format(fasta)

gff = snakemake.input.get("gff", "")
if gff:
    gff = "--gff {}".format(gff)

if cache:
    entrypath = get_only_child_dir(get_only_child_dir(Path(cache)))
    species = entrypath.parent.name
    release, build = entrypath.name.split("_")
    cache = (
        "--offline --cache --dir_cache {cache} --cache_version {release} --species {species} --assembly {build}"
    ).format(cache=cache, release=release, build=build, species=species)

shell(
    "(bcftools view {snakemake.input.calls} | "
    "vep {extra} {fork} "
    "--format vcf "
    "--vcf "
    "{cache} "
    "{gff} "
    "{fasta} "
    "--dir_plugins {plugins} "
    "{load_plugins} "
    "--output_file STDOUT "
    "--stats_file {stats} | "
    "bcftools view -O{fmt} > {snakemake.output.calls}) {log}"
)
Python Snakemake BCFtools Variant Effect Predictor (VEP) From line 1 of annotate/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2020, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"

from pathlib import Path
from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
    "vep_install --AUTO cf "
    "--SPECIES {snakemake.params.species} "
    "--ASSEMBLY {snakemake.params.build} "
    "--VERSION {snakemake.params.release} "
    "--CACHEDIR {snakemake.output} "
    "--CONVERT "
    "--NO_UPDATE "
    "{extra} {log}"
)
Python Snakemake From line 1 of cache/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2020, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"

import sys
from pathlib import Path
from urllib.request import urlretrieve
from zipfile import ZipFile
from tempfile import NamedTemporaryFile

if snakemake.log:
    sys.stderr = open(snakemake.log[0], "w")

outdir = Path(snakemake.output[0])
outdir.mkdir()

with NamedTemporaryFile() as tmp:
    urlretrieve(
        "https://github.com/Ensembl/VEP_plugins/archive/release/{release}.zip".format(
            release=snakemake.params.release
        ),
        tmp.name,
    )

    with ZipFile(tmp.name) as f:
        for member in f.infolist():
            memberpath = Path(member.filename)
            if len(memberpath.parts) == 1:
                # skip root dir
                continue
            targetpath = outdir / memberpath.relative_to(memberpath.parts[0])
            if member.is_dir():
                targetpath.mkdir()
            else:
                with open(targetpath, "wb") as out:
                    out.write(f.read(member.filename))
Python From line 1 of plugins/wrapper.py 
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wrapper:
    "0.74.0/bio/vep/annotate"
SnakeMake From line 25 of rules/annotation.smk 
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shell:
    "bedextract {wildcards.contig} {input} > {output}"
SnakeMake From line 10 of rules/calling.smk 
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wrapper:
    "0.59.0/bio/gatk/haplotypecaller"
SnakeMake From line 32 of rules/calling.smk 
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wrapper:
    "0.74.0/bio/gatk/combinegvcfs"
SnakeMake From line 46 of rules/calling.smk 
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wrapper:
    "0.74.0/bio/gatk/genotypegvcfs"
SnakeMake From line 60 of rules/calling.smk 
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wrapper:
    "0.74.0/bio/picard/mergevcfs"
SnakeMake From line 73 of rules/calling.smk 
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wrapper:
    "0.59.0/bio/gatk/selectvariants"
SnakeMake From line 11 of rules/filtering.smk 
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wrapper:
    "0.74.0/bio/gatk/variantfiltration"
SnakeMake From line 25 of rules/filtering.smk 
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wrapper:
    "0.74.0/bio/gatk/variantrecalibrator"
SnakeMake From line 38 of rules/filtering.smk 
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wrapper:
    "0.74.0/bio/picard/mergevcfs"
SnakeMake From line 55 of rules/filtering.smk 
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wrapper:
    "0.74.0/bio/trimmomatic/se"
SnakeMake From line 11 of rules/mapping.smk 
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wrapper:
    "0.74.0/bio/trimmomatic/pe"
SnakeMake From line 29 of rules/mapping.smk 
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wrapper:
    "0.74.0/bio/bwa/mem"
SnakeMake From line 47 of rules/mapping.smk 
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wrapper:
    "0.74.0/bio/picard/markduplicates"
SnakeMake From line 61 of rules/mapping.smk 
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wrapper:
    "0.74.0/bio/gatk/baserecalibrator"
SnakeMake From line 81 of rules/mapping.smk 
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wrapper:
    "0.74.0/bio/gatk/applybqsr"
SnakeMake From line 100 of rules/mapping.smk 
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wrapper:
    "0.74.0/bio/samtools/index"
SnakeMake From line 111 of rules/mapping.smk 
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wrapper:
    "0.74.0/bio/fastqc"
SnakeMake FastQC From line 9 of rules/qc.smk 
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wrapper:
    "0.74.0/bio/samtools/stats"
SnakeMake From line 20 of rules/qc.smk 
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wrapper:
    "0.74.0/bio/multiqc"
SnakeMake MultiQC From line 42 of rules/qc.smk 
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wrapper:
    "0.74.0/bio/reference/ensembl-sequence"
SnakeMake From line 12 of rules/ref.smk 
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wrapper:
    "0.74.0/bio/samtools/faidx"
SnakeMake From line 24 of rules/ref.smk 
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shell:
    "samtools dict {input} > {output} 2> {log} "
SnakeMake SAMtools From line 38 of rules/ref.smk 
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wrapper:
    "0.74.0/bio/reference/ensembl-variation"
SnakeMake From line 56 of rules/ref.smk 
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shell:
    "rbt vcf-fix-iupac-alleles < {input} | bcftools view -Oz > {output}"
SnakeMake BCFtools rust-bio-tools From line 70 of rules/ref.smk 
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wrapper:
    "0.74.0/bio/tabix"
SnakeMake tabix From line 84 of rules/ref.smk 
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wrapper:
    "0.74.0/bio/bwa/index"
SnakeMake From line 98 of rules/ref.smk 
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wrapper:
    "0.74.0/bio/vep/cache"
SnakeMake From line 111 of rules/ref.smk 
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wrapper:
    "0.74.0/bio/vep/plugins"
SnakeMake From line 122 of rules/ref.smk 
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shell:
    "(bcftools view --apply-filters PASS --output-type u {input} | "
    "rbt vcf-to-txt -g --fmt DP AD --info ANN | "
    "gzip > {output}) 2> {log}"
SnakeMake rust-bio-tools From line 14 of rules/stats.smk 
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script:
    "../scripts/plot-depths.py"
SnakeMake From line 36 of rules/stats.smk 
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import sys
sys.stderr = open(snakemake.log[0], "w")

import common
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import seaborn as sns

calls = pd.read_table(snakemake.input[0], header=[0, 1])
samples = [name for name in calls.columns.levels[0] if name != "VARIANT"]
sample_info = calls.loc[:, samples].stack([0, 1]).unstack().reset_index(1, drop=False)
sample_info = sample_info.rename({"level_1": "sample"}, axis=1)

sample_info = sample_info[sample_info["DP"] > 0]
sample_info["freq"] = sample_info["AD"] / sample_info["DP"]
sample_info.index = np.arange(sample_info.shape[0])

plt.figure()

sns.stripplot(x="sample", y="freq", data=sample_info, jitter=True)
plt.ylabel("allele frequency")
plt.xticks(rotation="vertical")

plt.savefig(snakemake.output.freqs)

plt.figure()

sns.stripplot(x="sample", y="DP", data=sample_info, jitter=True)
plt.ylabel("read depth")
plt.xticks(rotation="vertical")

plt.savefig(snakemake.output.depths)
Python Pandas numpy matplotlib seaborn common From line 1 of scripts/plot-depths.py
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Created: 10mo ago
Updated: 10mo ago
Maitainers: public
URL: https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling
Name: dna-seq-gatk-variant-calling
Version: v2.1.1
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