Snakemake implementation of data pre-processing for variant discovery from GATK Best Practices Workflows

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gatk4-data-processing
gatk4-data-processing
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Snakemake implementation of data pre-processing for variant discovery from GATK Best Practices Workflows

Code Snippets

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shell:
    "bwa mem -K 10000000 -P -o {output} -R '{params.rg}' {input.R1} {input.R2} {input.reference}"
SnakeMake BWA From line 19 of master/Snakefile 
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shell:
    "samtools sort -n -o {output} {input}"
SnakeMake SAMtools From line 27 of master/Snakefile 
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shell:
    "gatk MarkDuplicates -I {input} -O {output} --METRICS_FILE {sample}/MarkDuplicates.metrics.txt --VALIDATION_STRINGENCY SILENT --OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500 --ASSUME_SORT_ORDER 'queryname'"
SnakeMake gatk From line 36 of master/Snakefile 
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shell:
    "gatk SortSam -I {input} -O {output} --SORT_ORDER 'coordinate' --CREATE_INDEX false --CREATE_MD5_FILE false"
SnakeMake gatk From line 45 of master/Snakefile 
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shell:
    "gatk SetNmMdAndUqTags -I {input.bam} -O {output} --REFERENCE_SEQUENCE {input.reference} --CREATE_INDEX true"
SnakeMake gatk From line 55 of master/Snakefile 
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shell:
    "gatk BaseRecalibrator --use-original-qualities -I {input.bam} -O {output} -R {input.reference} --known-sites {input.indel} --known-sites {input.snp}"
SnakeMake gatk From line 67 of master/Snakefile 
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shell:
    "gatk ApplyBQSR -bqsr {input.table} -I {input.bam} -O {output} -R {input.reference} --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 --use-original-qualities --emit-original-quals true"
SnakeMake gatk From line 78 of master/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/yaotianran/gatk4-data-processing
Name: gatk4-data-processing
Version: 1
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Copyright: Public Domain
License: GNU General Public License v3.0
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