ngs_SNP

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.