Number of sites in .mafs.gz different from angsd
bvaditi opened this issue · 1 comments
bvaditi commented
Hi, is the number of sites in .mafs.gz file supposed to be different from those in angsd log file? For one of my populations I get a different value when counted with wc -l of .mafs.gz. For all other populations the number of sites in angsd log file and .mafs.gz are same
fgvieira commented
The number of sites can be different between ngsF and angsd, but it should be quite similar. How many sites do you get for each case?