Penn SCAP-T Pipeline: Documentation
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Module: SNP
Run SNP calling on the sorted bam file (ie sampleID/bowtie).
Usage:
ngs.sh snp [-i inputDir] -s species sampleID
Input:
sampleID/inputDir/sampleID.sorted.bam
Output:
sampleID/snp/sampleID.filtered.vcf
sampleID/snp/sampleID.bigWig
Requires:
freebayes ( https://github.com/ekg/freebayes )
bedtools ( http://bedtools.readthedocs.org/en/latest/ )
Kent sources ( http://genomewiki.ucsc.edu/index.php/Kent_source_utilities )
Options:
-i inputDir - directory with unaligned reads (default: bowtie)
-s species - species from repository: /lab/repo/resources/snp
Run SNP calling on the sorted bam file (ie sampleID/bowtie). Output is placed in the directory sampleID/snp.