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hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
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QUAL score of '.' #128

Open jgbaum opened 6 years ago

jgbaum commented 6 years ago

Hi,

We've been using Speedseq for quite some time and a question recently arose as to the meaning of QUAL scores that are a period (.). For example:

5   157481885   .   C   T   .   PASS    SSC=28.913;TYPE=snp GT:GQ:DP:RO:QR:AO:QA:GL 0/0:99:279:279:9865:0:0:0,-83.9874,-887.737 0/0:99:410:388:13804:22:756:0,-55.0744,-1173.72

Any information would be appreciated, including guidance on whether these should be filtered from downstream analysis. As an FYI, we use this version (2cb0fb8adb9fa9c429da81b211d39050ed368fdc) from Jun 20, 2016.

I thought it might be an issue related to Freebayes, and posted an issue there (https://github.com/ekg/freebayes/issues/478), but was told that it must be due to downstream processing by Speedseq.

Thanks and happy to provide more information, if necessary.

-Jason

jgbaum commented 6 years ago

Checking in on this. Any help would be much appreciated!