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lskatz / lyve-SET

:dancer: :palm_tree: LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
MIT License
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Masking in SNP-calling stage too #33

Closed lskatz closed 9 years ago

lskatz commented 9 years ago

Masking in the read-mapping stage only results in removing reads that are only in the masked regions. It does not remove reads that are overlapping but that are anchored in the unmasked regions. Therefore, masking also has to be done in the SNP-calling step.

lskatz commented 9 years ago

Actually due to the way that varscan works with mpileup, I'm not completely sure this is necessary. I'll have to look into it further

lskatz commented 9 years ago

I put this idea into filterMatrix.pl using Number::Range. This Perl module has since been included in the lib directory.

lskatz commented 9 years ago

Ok this has been done