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.
SNP calling
SNP Calling
Likelihood ratio test
supply -doSNP 1 Then the MAF estimate(s) given by -doMaf INT, will be used for a like ratio test
chromo position major minor knownEM pK-EM nInd 21 9719770 T A 0.000009 -0.000018 1 21 9719771 T A 0.000001 -0.000003 1 21 9719772 C A 0.000001 -0.000003 1 21 9719773 T A 0.000002 -0.000010 2 21 9719774 G A 0.000002 -0.000010 2 21 9719775 A C 0.000004 -0.000022 2 21 9719776 G A 0.000002 -0.000010 2 21 9719777 A C 0.000002 -0.000013 2