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Number of sites in .mafs.gz different from angsd #18

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bvaditi opened this issue Dec 25, 2021 · 1 comment
Open

Number of sites in .mafs.gz different from angsd #18

bvaditi opened this issue Dec 25, 2021 · 1 comment

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@bvaditi
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bvaditi commented Dec 25, 2021 •
edited by fgvieira
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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 fgvieira changed the title 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. Number of sites in .mafs.gz different from angsd Dec 28, 2021
@fgvieira
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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?

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@fgvieira @bvaditi