Fastq to bam mapping pipeline with marked duplicates, indexing, and insert size metric collection

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bwa_mem_mapping
bwa_mem_mapping
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Fastq to bam mapping pipeline with marked duplicates, indexing, and insert size metric collection

This is a Snakemake-based pipeline for mapping with BWA mem. The pipeline automatically marks duplicates, indexes bams, and calculates insert size metrics, all of which are useful for downstream analysis. The Snakefile is derived from johanneskoester's example here: https://bitbucket.org/johanneskoester/snakemake-workflows/src/e03c8a9fb7f256ed498b0a5984e9ae738a8f22e1/bio/ngs/rules/mapping/bwa_mem.rules?at=master

Code Snippets

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shell:
    "samtools flagstat {input[0]} > {output}"
SnakeMake SAMtools From line 78 of master/Snakefile 
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shell:
    "samtools idxstats {input[0]} > {output}"
SnakeMake SAMtools From line 87 of master/Snakefile 
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shell:
    """java -Xmx8G -jar $PICARD_DIR/CollectInsertSizeMetrics.jar I={input} O={output} H={output}.hist.pdf"""
SnakeMake From line 95 of master/Snakefile 
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shell: "samtools index {input}"
SnakeMake SAMtools From line 103 of master/Snakefile 
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run:
    if len(input) > 1:
        shell("samtools merge -p -@ 8 {output} {input}")
    else:
        shell("rsync --bwlimit=50000 {input} {output}")
SnakeMake SAMtools From line 110 of master/Snakefile 
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shell:
    """set -eo pipefail
       run-bwamem -t {params.bwa_threads} -dso $TMPDIR/tmp {input[0]} {input[1]} | bash
       rsync --bwlimit=50000 $TMPDIR/tmp.aln.bam {output}
       samtools index {output}"""
SnakeMake SAMtools From line 131 of master/Snakefile 
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shell:
    """set -eo pipefail
    bwa mem {params.custom} -R '@RG\\tID:{params.flowcell}_{wildcards.lane}\\tSM:{params.sample}\\tLB:{params.sample}\\tPL:{config[platform]}\\tPU:{params.flowcell}' \
        -t {params.bwa_threads} {input} 2> {log} | \
    samblaster | \
    samtools sort -@ {params.samtools_threads} -m {params.samtools_memory} -O bam -T $TMPDIR/{wildcards.lane} -o {output}
    samtools index {output}"""
SnakeMake SAMtools BWA SAMBLASTER From line 153 of master/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/bnelsj/bwa_mem_mapping
Name: bwa_mem_mapping
Version: 1
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Copyright: Public Domain
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