Fusarium Genome DNA-seq QC, Alignment, and Variant Calling Workflow Using Snakemake

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fusarium_workflow
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Fusarium_workflow

A basic snakemake file for QC, Alingment and Variant calling on DNAseq data of F.oxy.genome needs conda and snakemake to run

snakemake --use-conda -j {no-of-threads}

Code Snippets

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shell:
    "mkdir -p fastqc_reports && fastqc {input.read1} {input.read2} {input.trim1} {input.trim2} -o fastqc_reports"
SnakeMake FastQC From line 34 of main/Snakefile 
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shell:
    "mkdir -p trimmed_reads && \
    fastp -i {input.read1} -o {output.out1}\
    -I {input.read2} -O {output.out2}"
SnakeMake fastp From line 46 of main/Snakefile 
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shell:
    "mkdir -p bowtie_index && \
    bowtie2-build {input} {params}"
SnakeMake Bowtie 2 From line 65 of main/Snakefile 
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shell:
    "mkdir -p aligned_files && \
    bowtie2 -x {params} -1 {input.read1} -2 {input.read2} -S {output}"
SnakeMake Bowtie 2 From line 85 of main/Snakefile 
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shell:
    "samtools view --bam {input.sam} |  samtools sort - > {output.sorted_bam} && \
    samtools index {output.sorted_bam}"
SnakeMake SAMtools From line 97 of main/Snakefile 
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shell:
    "{gatkDir}/gatk CreateSequenceDictionary -R {input} && \
    samtools faidx {input}"
SnakeMake SAMtools gatk From line 109 of main/Snakefile 
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shell:
    "mkdir -p MD_metrics && \
    picard MarkDuplicates -I {input} -M {output.metric} -O {output.md}"
SnakeMake Picard From line 121 of main/Snakefile 
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shell:
    "picard SortSam -I {input} -O {output.bam} -SO coordinate"
SnakeMake Picard From line 132 of main/Snakefile 
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shell:
    "picard AddOrReplaceReadGroups -I {input.sorted_bam} -O {output.sorted_rg_bam} \
    -LB {wildcards.sample} -PL illumina -PU null -SM {wildcards.sample} && \
    samtools index {output.sorted_rg_bam}"
SnakeMake SAMtools Picard From line 142 of main/Snakefile 
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shell:
    "mkdir -p VCF && \ 
    {gatkDir}/gatk HaplotypeCaller -I {input.bam} -R {input.ref} -O {output} -ploidy 1"
SnakeMake gatk From line 157 of main/Snakefile 
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shell:
    "{gatkDir}/gatk VariantFiltration \
    -V {input.vcf} \
    -O {output} \
    -filter "QD<2.0 && AF<1.0 && FS>6.0 && MQ<40.0 && MQRankSum<-12.5 && ReadPosRankSum<-8.0" \
    --filter-name "my_filter"
SnakeMake gatk From line 168 of main/Snakefile 
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shell:
    "{gatkDir}/gatk SelectVariants \
     -R {input.ref} \
     -V {input.vcf} \
     --select-type-to-include SNP \
     -O {output}"
SnakeMake gatk From line 185 of main/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/ravenclown/Fusarium_workflow
Name: fusarium_workflow
Version: 1
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Copyright: Public Domain
License: None
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