Filters

In most analysis you are only interested in a subset of sites and not all sites. Currently we have the following filter options.

-minMaf float

only work with sites with a maf above 'float'

-minKeepInd int

only work with sites with information from atleast int individiduals

-minLRT float

only work with sits with an LRT>float

First we do a run with no filters

./angsd  -doMaf 2 -doMajorMinor 1 -out TSK -bam bam.filelist -GL 1 -r 1:
...
head TSK.mafs
head TSK.mafs 
chromo	position	major	minor	knownEM	nInd
1	13999919	A	C	0.000008	1
1	13999920	G	A	0.000008	1
1	13999921	G	A	0.000008	1
1	13999922	C	A	0.000008	1
1	13999923	A	C	0.000008	1
1	13999924	G	A	0.000008	1
1	13999925	G	A	0.000008	1
1	13999926	A	C	0.000008	1
1	13999927	G	A	0.000008	1

Deprecated options

These options should either be included (as is) or be discarded

-minDepth

-maxDepth