Workflow Steps and Code Snippets

987 tagged steps and code snippets that match keyword BCFtools

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

shell:
    "rbt vcf-fix-iupac-alleles < {input} | bcftools view -Oz > {output}"

SnakeMake BCFtools rust-bio-tools From line 70 of rules/ref.smk

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

shell:
    "rbt vcf-fix-iupac-alleles < {input} | bcftools view -Oz > {output}"

SnakeMake BCFtools rust-bio-tools From line 70 of rules/ref.smk

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

shell:
    "rbt vcf-fix-iupac-alleles < {input} | bcftools view -Oz > {output}"

SnakeMake BCFtools rust-bio-tools From line 70 of rules/ref.smk

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

shell:
    "rbt vcf-fix-iupac-alleles < {input} | bcftools view -Oz > {output}"

SnakeMake BCFtools rust-bio-tools From line 70 of rules/ref.smk

Bioinfo Macro Host Genome Short Variant Discovery Workflow

shell:
    "bcftools index {input} 2> {log} 1>&2"

SnakeMake BCFtools From line 11 of rules/bcftools.smk

shell:
    """
    bcftools concat \
        --output {output} \
        --output-type z9 \
        --threads {threads} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake BCFtools From line 360 of rules/gatk4.smk

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

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

shell:
    """
    bcftools concat \
        --output-type z9 \
        --output {output.vcf} \
        {input.vcf} \
    2> {log} 1>&2
    """

SnakeMake BCFtools From line 110 of rules/swaps.smk

shell:
    """
    bcftools gtcheck \
        {input.vcf} \
    > {output.tsv} 2> {log}
    """

SnakeMake BCFtools From line 130 of rules/swaps.smk

tool / biotools

BCFtools

bcftools

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

References: