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Good loci lost during phasing #17

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brunoasm opened this issue Oct 16, 2019 · 0 comments
Open

Good loci lost during phasing #17

brunoasm opened this issue Oct 16, 2019 · 0 comments

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@brunoasm
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I noticed that some of my samples that sequenced at highest coverage have several loci missing after phasing. After some testing with samtools, I think the problem is that by default max coverage is set to 256 (flag -D). It seems SECAPR code does not change this flag, so maybe setting it to something higher will eliminate the problem.
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@brunoasm