Contamination

Angsd can estimate contamination, but only for chromosomes that exists in one genecopy (eg chrX for males). This method requires a list of HapMap sites along with their frequency and we also recommend to discard regions with low mappability.

We have included a mappability and HapMap files for chrX these are found in the RES subfolder of the angsd source package. So if you are working with humans, and your sample is a male then you can estimate the contamination with the follow two commands.

• First we generate a binary count file for chrX for a single BAM file (ANGSD cprogram)
• Then we do a fisher test for finding a p-value, and jackknife to get an estimate of contamination (Rprogram)

An example are found below:

./angsd -i my.bam -r X: -doCounts 1  -iCounts 1 -minMapQ 30 -minQ 20