Candy lab analysis workflow

public 1yr ago 0 bookmarks

View Workflow

Help improve this workflow!

This workflow has been published but could be further improved with some additional meta data:

Keyword(s) in categories input, output, operation, topic

You can help improve this workflow by suggesting the addition or removal of keywords, suggest changes and report issues, or request to become a maintainer of the Workflow .

Automation of the workflow originally developped by Irene Lobon

Mutect2 variant calling
Quality filtering
Multi sample merging and rescuing
.. TO BE ADDED: annotation

Code Snippets

shell:
    "java -jar $EBROOTGATK/gatk-package-4.1.8.1-local.jar Mutect2 \
    --native-pair-hmm-threads {threads} \
    -R {input.ref} \
    -L {input.intv} \
    -I {input.tb} \
    -I {input.nb} \
    -normal {params.nn} \
    -germline-resource {input.gr} \
    -pon {input.pon} \
    --f1r2-tar-gz {output.n} \
    -O {output.v}"

SnakeMake From line 51 of pipeline/Snakefile

shell:
    "java -jar $EBROOTGATK/gatk-package-4.1.8.1-local.jar LearnReadOrientationModel \
    -I {input} \
    -O {output}"

SnakeMake From line 81 of pipeline/Snakefile

shell:
    """
    java -jar $EBROOTGATK/gatk-package-4.1.8.1-local.jar FilterMutectCalls \
    -R {input.r} \
    -V {input.v} \
    --ob-priors {input.priors} \
    -O {output.v}
    """

SnakeMake From line 108 of pipeline/Snakefile

shell:
    "tabix -p vcf {input}"

SnakeMake tabix From line 134 of pipeline/Snakefile

shell:
    """
    #echo "##INFO=<ID=AS_FilterStatus,Number=A" | sed "s/##INFO=<ID=AS_FilterStatus,Number=A/##INFO=<ID=AS_FilterStatus,Number=1/" && touch {output.v} && touch {output.i}
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools norm -m -any {input.v} | sed "s/##INFO=<ID=AS_FilterStatus,Number=A/##INFO=<ID=AS_FilterStatus,Number=1/" | bgzip > {output.v}
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools tabix {output.v}
    """

SnakeMake BCFtools tabix From line 157 of pipeline/Snakefile

shell:
    """
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools view \
    -i '(ROQ>{params.ROQ} & AD[1:1]>{params.AD}) & (FILTER="PASS" | FILTER="clustered_events" )' -Oz -o {output.v} {input.v}
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools tabix {output.v}
    """

SnakeMake BCFtools tabix From line 188 of pipeline/Snakefile

shell:
    """
    cp {input.v} {output.v}
    cp {input.i} {output.i}
    """

SnakeMake From line 211 of pipeline/Snakefile

shell:
    """
    zcat {input.v} | grep -v "^#" | cut -f1-5 | sort -V | uniq > {output}
    """

SnakeMake From line 235 of pipeline/Snakefile

shell:
    """
    zcat {input.v} | grep "^#" | bgzip >{output.v}
    for x in $(seq 1 1000 $(wc -l {input.pos} | awk '{{print $1}}'))
    do
    y=$((x+999))
    zcat {input.v} | grep -v "^#" | grep --line-buffered -f <(sed -n "${{x}},${{y}}p" {input.pos}) - | bgzip >> {output.v}
    done
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools tabix {output.v}
    """

SnakeMake BCFtools tabix From line 261 of pipeline/Snakefile

shell:
    """
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools merge -0 -Oz -o {output.v} --force-samples {input.v}
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools tabix {output.v}
    """

SnakeMake BCFtools tabix From line 292 of pipeline/Snakefile

shell:
    """
    echo {params.GL} > {output.s}
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools query -l {input.v} | grep -v {params.GL} >> {output.s}
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools view -S {output.s} {input.v} -Oz -o {output.v1} 
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools sort {output.v1} -Oz -o {output.v2}
    tabix -p vcf {output.v2}
    """

SnakeMake BCFtools tabix From line 321 of pipeline/Snakefile

shell:
    """
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools norm -m -any {input.v} | bgzip > {output}
    """

SnakeMake BCFtools From line 348 of pipeline/Snakefile

shell:
    """
    # Make a list of bams in VCF order
    echo {input.nb} > {output.bamlist}
    for i in {input.tb}; do echo $i >> {output.bamlist}; done
    /nemo/lab/turajlics/home/users/fidanr/bcftools/bin/bcftools query -l {input.v} >> {output.s}
    while read i; do grep $i {output.bamlist} >> {output.obamlist}; done< {output.s}
    #Genotype (SNVs, MNVs and indels)
    python3.6 {params.res} {input.v} {output.obamlist} {output.v}
    """