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.
SnpFilters
Angsd has different snpfilters.
- SB1 strand bias1
- SB2 strand bias2
- SB3 strand bias3
- deviation from HWE
- Wilcox rank sum test for position in read
The 3 strand bias filters are described here: http://www.biomedcentral.com/1471-2164/13/666
The deviation from HWE is described in http://www.ncbi.nlm.nih.gov/pubmed/23950147
The wilcox rank sum test is not described anywhere