min_AQ1 has no effect when min_AQ2 is zero

dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects

Apache License 2.0

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min_AQ1 has no effect when min_AQ2 is zero #165

Closed tedyun closed 5 years ago

tedyun commented 5 years ago

My name is Ted Yun and I'm in Genomics team at Google. My coworkers and I have found that when GLnexus is run with the two different set of parameters: min_AQ1 = 30, min_AQ2 = 0 and min_AQ1 = 0, min_AQ2 = 0, it produces identical results.

I believe I've found the cause of the issue and have created a pull request containing a fix - https://github.com/dnanexus-rnd/GLnexus/pull/164 Please take a look. Thank you!

Regards, Ted

tedyun commented 5 years ago

New pull request - https://github.com/dnanexus-rnd/GLnexus/pull/167

mlin commented 5 years ago

@tedyun I merged that change -- based on the other Q&A I assume it's not urgent to cut a new released version, but LMK otherwise.

Thank you for the report and PR, hope there's more where that came from :smile:

tedyun commented 5 years ago

@mlin Thank you! :)