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No SNPs displayed when sequence is from 'b' tag #36

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cmdcolin opened this issue May 21, 2019 · 2 comments
Open

No SNPs displayed when sequence is from 'b' tag #36

cmdcolin opened this issue May 21, 2019 · 2 comments

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@cmdcolin
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This is a follow up from the previous issue of #34

Currently when large blocks of sequence are loaded from 'b', we don't have SNPs in this file. I don't know if we need to manually compare it with a seqFetch to see if SNPs exist?
@cmdcolin
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Possibly this is a 'samtools calmd' analog in CRAM form too. We will follow up in email with sacha

@cmdcolin
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cmdcolin commented Jun 5, 2019

Ref here https://sourceforge.net/p/samtools/mailman/message/36681818/

Apparently samtools can resolve SNPs between this and a refseq from what I can tell, creating both a MD and CIGAR string from samtools view file.cram

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@cmdcolin