filterSAMbyVCF is a Pascal command line program to separate allele-specific reads from a SAM file.
This program extracts reads from SAM file according to SNPs from VCF file.
Extracted reads have ALT allele at the position given in VCF file.
Usage with UNIX/Linux/MacOS: ./filterSAMbyVCF vcfFile.vcf samFile.sam
Usage with Windows: filterSAMbyVCF.exe vcfFile.vcf samFile.sam
No warranty of any kind is provided. Use at your own risk.
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