Workflow Steps and Code Snippets

3191 tagged steps and code snippets that match keyword SAMtools

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

shell:
    "samtools dict {input} > {output} 2> {log} "

SnakeMake SAMtools From line 38 of rules/ref.smk

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

shell:
    "samtools dict {input} > {output} 2> {log} "

SnakeMake SAMtools From line 38 of rules/ref.smk

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

shell:
    "samtools dict {input} > {output} 2> {log} "

SnakeMake SAMtools From line 38 of rules/ref.smk

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

shell:
    "samtools dict {input} > {output} 2> {log} "

SnakeMake SAMtools From line 38 of rules/ref.smk

WES analysis pipeline

shell:
    """
    gatk SamToFastq -I {input.bam} -F /dev/stdout -INTER true -NON_PF true \
    | \
    bwa mem -p -v 3 -t {threads} -T 0 \
        {input.ref} /dev/stdin - 2> >(tee {log} >&2) \
    | \
    samtools view -Shb -o {output}
    """

SnakeMake SAMtools gatk BWA From line 50 of rules/preprocessing.smk

shell:
    """
    samtools flagstat {input} > {output}
    """

SnakeMake SAMtools From line 166 of rules/preprocessing.smk

Snakemake pipeline for detection limit test from laser-microdissected samples

shell:
    """
    if [[ {params.is_paired} = "True" ]] ; then
        (bowtie2 \
            -x {input.mock} \
            -1 {input.forward_} \
            -2 {input.reverse_} \
            --threads {threads} \
            --rg-id '{params.rg_id}' \
            --rg '{params.rg_extra}' \
            {params.extra} \
        | samtools sort \
            --threads {threads} \
            -m {params.samtools_mem} \
        | samtools rmdup - - \
        | samtools view \
            --reference {input.reference} \
            --output {output.cram} \
            --output-fmt cram,level=9,nthreads={threads} \
            --write-index \
        ) 2> {log} 1>&2
    else
        (bowtie2 \
            -x {input.mock} \
            -U {input.forward_} \
            --threads {threads} \
            --rg-id '{params.rg_id}' \
            --rg '{params.rg_extra}' \
            {params.extra} \
        | samtools sort \
            --threads {threads} \
            -m {params.samtools_mem} \
        | samtools rmdup -s - - \
        | samtools view \
            --reference {input.reference} \
            --output {output.cram} \
            --output-fmt cram,level=9,nthreads={threads} \
            --write-index \
        ) 2> {log} 1>&2
    fi
    """

SnakeMake SAMtools From line 59 of rules/bowtie2_hosts.smk

shell:
    """
    if [[ {params.is_paired} = "True" ]] ; then
        (samtools view \
            --reference {input.reference} \
            --threads {threads} \
            -u \
            -o /dev/stdout \
            -f 12 \
            {input.cram} \
        | samtools fastq \
            -1 {output.forward_} \
            -2 {output.reverse_} \
            -0 /dev/null \
            -c 9 \
            --threads {threads} \
        ) 2> {log} 1>&2
    else
        (samtools view \
            --reference {input.reference} \
            --threads {threads} \
            -u \
            -o /dev/stdout \
            -f 4 \
            {input.cram} \
        | samtools fastq \
            -0 {output.forward_} \
            -c 9 \
            --threads {threads} \
        ) 2> {log} 1>&2
    fi
    """

SnakeMake SAMtools From line 123 of rules/bowtie2_hosts.smk

shell:
    """
    if [[ {params.is_paired} == "True" ]] ; then
        (bowtie2 \
            -x {input.mock} \
            -1 {input.forward_} \
            -2 {input.reverse_} \
            --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} \
            --write-index \
        ) 2> {log} 1>&2
    else
        (bowtie2 \
            -x {input.mock} \
            -U {input.forward_} \
            --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} \
            --write-index \
        ) 2> {log} 1>&2
    fi
    """

SnakeMake SAMtools From line 59 of rules/bowtie2_mags.smk

shell:
    "samtools flagstats {input.cram} > {output.txt} 2> {log}"

SnakeMake SAMtools From line 12 of rules/samtools.smk

tool / biotools

SAMtools

samtools

SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.

References: