Simple snakemake workflow for SNP calling, annotation and visualization.

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Simple snakemake workflow for SNP calling, annotation and visualization.

Code Snippets

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shell:
    """
    echo "Input Fastq: {input.fq} "
    fastqc -o 010.fastqc {input.fq}
    """
SnakeMake FastQC From line 26 of main/Snakefile 
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shell:
    """
    bwa mem {params.ref} {input.fq} \
        | samtools sort - \
        > {output.bam}
    samtools index {output.bam}
    """
SnakeMake SAMtools BWA From line 43 of main/Snakefile 
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shell:
    """
    bcftools mpileup -Ou -f {input.ref} {input.bams} \
         | bcftools call -mv -Ov -o {output.vcf}
    """
SnakeMake BCFtools From line 59 of main/Snakefile 
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shell:
    """
    ( cat {input.vcf} \
       | vt decompose - \
       | vt normalize -n -r {input.ref} - \
       | vt uniq - \
       | vt view -f "QUAL>20" -h - \
       > {output.vcf} )
    """
SnakeMake vt From line 74 of main/Snakefile 
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shell:
    """
    mkdir -p 050.snpeff

    java -Xmx4096m -jar \
        {params.snpeff_jar} eff GRCh38.99 \
        -dataDir {params.snpeff_db_folder} \
        {input.vcf} > {output.vcf}

    # move output files to the snpeff output folder
    mv snpEff_genes.txt snpEff_summary.html 050.snpeff
    """
SnakeMake From line 100 of main/Snakefile 
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shell:
    """
    mkdir -p 060.stats

    bcftools stats -s - {input.vcf} > {output.stats}

    plot-vcfstats -P -p 060.stats {output.stats}
    """
SnakeMake BCFtools vcfstats From line 121 of main/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/domivika/Snakemake
Name: snakemake
Version: 2
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Other Versions:
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Downloaded: 0
Copyright: Public Domain
License: None
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