abcontamination

This software (plot_allele_balance_find_contamination.pl) produces an allele balance histogram and assesses DNA contamination of a single sample in a VCF file (vers. 3 & 4) that has been annotated in the info field for the AB=<num> metric in the range 0 - 1.0. It requires that the R statistical package is installed and in your path and can be run on the Linux, Unix or Mac computer. It does not work on multi-sample VCF files. If your VCF is not annotated for AB=<num> you may do this using the Broad's GATK annotation functions, the VCF file and the sample's bam file.