ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
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.
Angsd comes with these two files in the RES/ subfolder and these are called:
An example are found below: