Bioinfo Macro Host Genome Short Variant Discovery Workflow

public public 1yr ago 0 bookmarks
View Workflow
Report
bioinfo_macro_host_genomics
bioinfo_macro_host_genomics
bioinfo_macro_host_genomics
View Workflow

A Snakemake workflow for Short Variant Discovery in Host Genomes

Usage

  • Test that it works:

    • Make sure you have installed snakemake, samtools and bcftools. Either

      • install them with conda/mamba : conda install -c bioconda samtools bcftools ).

      • or create an environment ( conda create -n 3dohg -c bioconda snakemake samtools bcftools ), and activate it ( conda activate 3dohg )

    • Generate mock data with bash workflow/scripts/generate_mock_data.sh

    • Run the pipeline: snakemake --use-conda --jobs 8 all . It will download all the necesary software through conda. It should take less than 5 minutes.

  • Run it with your own data:

    • Edit config/samples.tsv and add your samples and where are they located.

    • Edit config/features.tsv with information regarding the reference you are using.

    • Run the pipeline: snakemake --use-conda --jobs 8 all .

    • (slurm users): ./run_slurm

Features

DAG

host_genomics_pipeline

Code Snippets

11
12
shell:
    "bcftools index {input} 2> {log} 1>&2"
SnakeMake BCFtools From line 11 of rules/bcftools.smk 
29
30
31
32
33
34
35
36
37
shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {params.output_path} \
    2> {log} 1>&2
    """
SnakeMake Bowtie 2 From line 29 of rules/bowtie2.smk 
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
shell:
    """
    (bowtie2 \
        -x {params.index_prefix} \
        -1 {input.forward_} \
        -2 {input.reverse_} \
        -U {input.unpaired1},{input.unpaired2} \
        --threads {threads} \
        --rg-id '{params.rg_id}' \
        --rg '{params.rg_extra}' \
        {params.extra} \
    | samtools sort \
        -l 9 \
        -M \
        -m {params.samtools_mem} \
        -o {output.cram} \
        --reference {input.reference} \
        --threads {threads} \
    ) 2> {log} 1>&2
    """
SnakeMake SAMtools From line 78 of rules/bowtie2.smk 
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
shell:
    """
    fastp \
        --in1 {input.forward_} \
        --in2 {input.reverse_} \
        --out1 {output.forward_} \
        --out2 {output.reverse_} \
        --unpaired1 {output.unpaired1} \
        --unpaired2 {output.unpaired2} \
        --html {output.html} \
        --json {output.json} \
        --compression 1 \
        --verbose \
        --adapter_sequence {params.adapter_forward} \
        --adapter_sequence_r2 {params.adapter_reverse} \
        --thread {threads} \
        {params.extra} \
    2> {log} 1>&2
    """
SnakeMake fastp From line 27 of rules/fastp.smk 
12
13
shell:
    "fastqc {input} 2> {log} 1>&2"
SnakeMake FastQC From line 12 of rules/fastqc.smk 
23
24
25
26
27
28
29
30
31
32
shell:
    """
    gatk BaseRecalibrator \
        {params.extra} \
        --input {input.bam} \
        --reference {input.reference} \
        --known-sites {input.known_sites} \
        --output {output.table} \
    2> {log} 1>&2
    """
SnakeMake gatk From line 23 of rules/gatk4.smk 
65
66
67
68
69
70
71
72
73
74
shell:
    """
    gatk ApplyBQSR \
        {params.extra} \
        --input {input.bam} \
        --reference {input.reference} \
        --bqsr-recal-file {input.table} \
        --output {output.bam} \
    2> {log} 1>&2
    """
SnakeMake gatk From line 65 of rules/gatk4.smk 
123
124
125
126
127
128
129
130
131
132
133
shell:
    """
    gatk HaplotypeCaller \
        {params.extra} \
        --reference {input.reference} \
        --input {input.bam} \
        --output {output.gvcf_gz} \
        --emit-ref-confidence GVCF \
        -ploidy {params.ploidy} \
    2> {log} 1>&2
    """
SnakeMake gatk From line 123 of rules/gatk4.smk 
169
170
171
172
173
174
175
176
177
shell:
    """
    gatk CombineGVCFs \
        {params.extra} \
        {params.variant_line} \
        --reference {input.reference} \
        --output {output.vcf_gz} \
    2> {log} 1>&2
    """
SnakeMake gatk From line 169 of rules/gatk4.smk 
205
206
207
208
209
210
211
212
213
shell:
    """
    gatk GenotypeGVCFs \
        {params.extra} \
        --variant {input.vcf_gz} \
        --reference {input.reference} \
        --output {output.vcf_gz} \
    2> {log} 1>&2
    """
SnakeMake gatk From line 205 of rules/gatk4.smk 
251
252
253
254
255
256
257
258
259
shell:
    """
    gatk CalculateGenotypePosteriors \
        {params.extra} \
        --output {output.vcf} \
        --variant {input.vcf} \
        --reference {input.reference} \
    2> {log} 1>&2
    """
SnakeMake gatk From line 251 of rules/gatk4.smk 
292
293
294
295
296
297
298
299
300
301
302
shell:
    """
    gatk VariantFiltration \
        {params.extra} \
        --reference {input.reference} \
        --variant {input.vcf} \
        --output {output.vcf} \
        --filter-expression '{params.filter_expression}' \
        --filter-name '{params.filter_name}' \
    2> {log} 1>&2
    """
SnakeMake gatk From line 292 of rules/gatk4.smk 
360
361
362
363
364
365
366
367
368
shell:
    """
    bcftools concat \
        --output {output} \
        --output-type z9 \
        --threads {threads} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake BCFtools From line 360 of rules/gatk4.smk 
18
19
20
21
22
23
24
25
26
27
shell:
    """
    samtools view \
        --bam \
        --uncompressed \
        --output {output.bam} \
        {input.cram} \
        {params.chromosome} \
    2> {log} 1>&2
    """
SnakeMake SAMtools From line 18 of rules/picard.smk 
57
58
59
60
61
62
63
64
65
66
67
shell:
    """
    picard MarkDuplicates \
        --INPUT {input.bam} \
        --OUTPUT {output.bam} \
        --METRICS_FILE {output.metrics} \
        --ASSUME_SORT_ORDER coordinate \
        --COMPRESSION_LEVEL 1 \
        --REFERENCE_SEQUENCE {input.reference} \
    2> {log} 1>&2
    """
SnakeMake Picard From line 57 of rules/picard.smk 
13
14
15
16
17
shell:
    """
    ln --symbolic $(readlink --canonicalize {input.forward_}) {output.forward_}
    ln --symbolic $(readlink --canonicalize {input.reverse_}) {output.reverse_}
    """
SnakeMake From line 13 of rules/reads.smk 
12
13
14
15
16
17
18
19
20
21
22
23
24
shell:
    """
    (gzip \
        --decompres \
        --stdout {input.fa_gz} \
    | bgzip \
        --compress-level 9 \
        --threads {threads} \
        --stdout \
        /dev/stdin \
    > {output.fa_gz} \
    ) 2> {log}
    """
SnakeMake From line 12 of rules/reference.smk 
38
39
40
41
42
43
44
shell:
    """
    (gzip -dc {input.vcf_gz} \
    | bgzip --threads {threads} \
    > {output.vcf_gz}) \
    2> {log}
    """
SnakeMake From line 38 of rules/reference.smk 
16
17
18
19
20
21
22
23
24
25
shell:
    """
    multiqc \
        --title {params.chromosome} \
        --force \
        --filename {params.chromosome} \
        --outdir {params.out_dir} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC From line 16 of rules/report_chromosome.smk 
24
25
26
27
28
29
30
31
32
33
shell:
    """
    multiqc \
        --title {params.library} \
        --force \
        --filename {params.library} \
        --outdir {params.out_dir} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC From line 24 of rules/report_library.smk 
13
14
15
16
17
18
19
20
21
22
shell:
    """
    multiqc \
        --filename reads \
        --title reads \
        --force \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC From line 13 of rules/report_step.smk 
37
38
39
40
41
42
43
44
45
46
shell:
    """
    multiqc \
        --title fastp \
        --force \
        --filename fastp \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC fastp From line 37 of rules/report_step.smk 
61
62
63
64
65
66
67
68
69
70
shell:
    """
    multiqc \
        --title bowtie2 \
        --force \
        --filename bowtie2 \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC Bowtie 2 From line 61 of rules/report_step.smk 
85
86
87
88
89
90
91
92
93
94
shell:
    """
    multiqc \
        --title picard \
        --force \
        --filename picard \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC Picard From line 85 of rules/report_step.smk 
109
110
111
112
113
114
115
116
117
118
shell:
    """
    multiqc \
        --title gatk4 \
        --force \
        --filename gatk4 \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC From line 109 of rules/report_step.smk 
133
134
135
136
137
138
139
140
141
142
shell:
    """
    multiqc \
        --title snpeff \
        --force \
        --filename snpeff \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC From line 133 of rules/report_step.smk 
11
12
shell:
    "samtools index {input} 2> {log} 1>&2"
SnakeMake SAMtools From line 11 of rules/samtools.smk 
25
26
shell:
    "samtools index {input} 2> {log} 1>&2"
SnakeMake SAMtools From line 25 of rules/samtools.smk 
39
40
shell:
    "samtools dict {input} --output {output} 2> {log} 1>&2"
SnakeMake SAMtools From line 39 of rules/samtools.smk 
53
54
shell:
    "samtools dict {input} --output {output} 2> {log} 1>&2"
SnakeMake SAMtools From line 53 of rules/samtools.smk 
67
68
shell:
    "tabix {input} 2> {log} 1>&2"
SnakeMake tabix From line 67 of rules/samtools.smk 
81
82
shell:
    "bgzip {input} 2> {log} 1>&2"
SnakeMake From line 81 of rules/samtools.smk 
96
97
shell:
    "samtools stats {input.bam} > {output.tsv} 2> {log}"
SnakeMake SAMtools From line 96 of rules/samtools.smk 
111
112
shell:
    "samtools stats {input.cram} > {output.tsv} 2> {log}"
SnakeMake SAMtools From line 111 of rules/samtools.smk 
126
127
shell:
    "samtools flagstats {input.bam} > {output.txt} 2> {log}"
SnakeMake SAMtools From line 126 of rules/samtools.smk 
141
142
shell:
    "samtools flagstats {input.cram} > {output.txt} 2> {log}"
SnakeMake SAMtools From line 141 of rules/samtools.smk 
156
157
shell:
    "samtools idxstats {input.bam} > {output.tsv} 2> {log}"
SnakeMake SAMtools From line 156 of rules/samtools.smk 
171
172
shell:
    "samtools idxstats {input.cram} > {output.tsv} 2> {log}"
SnakeMake SAMtools From line 171 of rules/samtools.smk 
12
13
14
15
16
17
18
19
shell:
    """
    snpEff download \
        {params.snpeff_db} \
        -dataDir {params.datadir} \
        -verbose \
    2> {log} 1>&2
    """
SnakeMake snpEff From line 12 of rules/snpeff.smk 
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
shell:
    """
    (snpEff ann \
        {params.snpeff_db} \
        -dataDir {params.datadir} \
        -csvStats {output.csv} \
        -verbose \
        -i vcf \
        -o gatk \
        {input.vcf} \
    | bgzip \
        --compress-level 9 \
        --stdout \
    > {output.vcf} \
    ) 2> {log} 1>&2

    mv {params.html} {output.html} 2>> {log} 1>&2
    """
SnakeMake gatk From line 43 of rules/snpeff.smk 
15
16
17
18
19
20
21
22
23
24
25
26
shell:
    """
    picard AddOrReplaceReadGroups \
        --INPUT {input.bam} \
        --OUTPUT {output.bam} \
        --RGLB {params.sample_library} \
        --RGPL illumina \
        --RGPU {params.sample_library} \
        --RGSM {params.sample_library} \
        --COMPRESSION_LEVEL 9 \
    2> {log} 1>&2
    """
SnakeMake Picard From line 15 of rules/swaps.smk 
50
51
52
53
54
55
56
57
58
59
60
61
62
shell:
    """
    (bcftools mpileup \
        --output-type z9 \
        --fasta-ref {input.reference} \
        {input} \
    | bcftools call \
        --variants-only \
        --multiallelic-caller \
        --output-type z9 \
        --output {output.vcf} ) \
    2> {log} 1>&2
    """
SnakeMake BCFtools From line 50 of rules/swaps.smk 
83
84
85
86
87
88
89
90
91
shell:
    """
    bcftools filter \
        --include 'QUAL>{params.min_qual}' \
        --output-type z9 \
        --output {output.vcf} \
        {input.vcf} \
    2> {log} 1>&2
    """
SnakeMake BCFtools From line 83 of rules/swaps.smk 
110
111
112
113
114
115
116
117
shell:
    """
    bcftools concat \
        --output-type z9 \
        --output {output.vcf} \
        {input.vcf} \
    2> {log} 1>&2
    """
SnakeMake BCFtools From line 110 of rules/swaps.smk 
130
131
132
133
134
135
shell:
    """
    bcftools gtcheck \
        {input.vcf} \
    > {output.tsv} 2> {log}
    """
SnakeMake BCFtools From line 130 of rules/swaps.smk 
148
149
150
151
152
153
154
shell:
    """
    Rscript workflow/scripts/plot_gtcheck.R \
        --infile {input} \
        --outfile {output} \
    2> {log} 1>&2
    """
SnakeMake From line 148 of rules/swaps.smk 
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
library(getopt)
library(tidyverse)

option_matrix <- matrix(
  c(
    "infile", "i", 1, "character",
    "outfile", "o", 1, "character"
  ),
  byrow = TRUE, ncol = 4
)

options <- getopt(option_matrix)



read_gtcheck <- function(gtcheck_filename) {
  read_tsv(
    file = gtcheck_filename,
    skip = 20,
    col_names = c(
      "dc", "query_sample", "genotyped_sample", "discordance", "log_p_hwe",
      "number_of_sites"
    )
  ) %>%
  select(-dc)
}

create_distance_matrix <- function(gtcheck_long) {
  gtcheck_diagonal <-
    gtcheck_long %>%
    select(query_sample, genotyped_sample) %>%
    mutate(discordance = 0) %>%
    pivot_longer(
      query_sample:genotyped_sample,
      names_to = "type",
      values_to = "query_sample"
    ) %>%
    select(query_sample) %>%
    mutate(
      genotyped_sample = query_sample,
      discordance = 0.0
    ) %>%
    distinct()

  gtcheck_upper <-
    gtcheck_long %>%
    select(query_sample, genotyped_sample, discordance)

  gtcheck_lower <-
    gtcheck_long %>%
    select(
      genotyped_sample = query_sample,
      query_sample = genotyped_sample,
      discordance
    )

  gtcheck_discordances <-
    bind_rows(gtcheck_diagonal, gtcheck_upper, gtcheck_lower) %>%
    arrange(query_sample)

  gtcheck_discordances_matrix <-
    gtcheck_discordances %>%
    pivot_wider(
      names_from = genotyped_sample,
      values_from = discordance
    ) %>%
    column_to_rownames("query_sample") %>%
    as.matrix()

  return(gtcheck_discordances_matrix)
}


if (!interactive()) {
  gtcheck_long <- read_gtcheck(options$infile)
  gtcheck_discordances_matrix <- create_distance_matrix(gtcheck_long)
  pdf(file = options$outfile, paper = "a4")
  heatmap(gtcheck_discordances_matrix)
  dev.off()
}
R tidyverse getopt From line 2 of scripts/plot_gtcheck.R
ShowHide 36 more snippets with no or duplicated tags.

Login to post a comment if you would like to share your experience with this workflow.

Do you know this workflow well? If so, you can request seller status , and start supporting this workflow.

Free

Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/3d-omics/Bioinfo_Macro_Host_Genomics
Name: bioinfo_macro_host_genomics
Version: 1
Badge:
workflow icon

Insert copied code into your website to add a link to this workflow.

Downloaded: 0
Copyright: Public Domain
License: MIT License
  • Future updates

Related Workflows

psychip_snakemake
Show Details View Workflow
ENCODE pipeline for histone marks developed for the psychENCODE project
public

public

psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project. The o...
raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
ncov_2
Show Details View Workflow
Near-real time tracking of SARS-CoV-2 in Connecticut
public

public

Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode
Free
28
cellranger-snakemake-gke
Show Details View Workflow
snakemake workflow to run cellranger on a given bucket using gke.
public

public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
atlas
Show Details View Workflow
ATLAS - Three commands to start analyzing your metagenome data
public

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics
Free
175
rna-seq-star-deseq2
Show Details View Workflow
RNA-seq workflow using STAR and DESeq2
public

public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41
dna-seq-gatk-variant-calling
Show Details View Workflow
This Snakemake pipeline implements the GATK best-practices workflow
public

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57