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Old 07-05-2013, 07:46 AM   #1
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Location: NY

Join Date: Feb 2013
Posts: 4
Default what is indelFS and indelQD in the filter column of VCF file

Newbie to VCF files of next gen seq.
Not sure if this is pipeline specific as I cannot find anything from googling the terms that explains what they are.

In the VCF file I received, in the filter column, a few possibilities are displayed -
VQSRTranchesSNP (with various percentiles)

It's easy to understand the former two but what are IndelFS and IndelQD as filters. What's the meaning of those SNPs identified with these two "filters" ? Specifically, are they
(a) likely "non-permissible" SNPs because they are identified when the sequence alignment suggests possible Indel ?
(b) likely SNPs but a high percentage of samples show Indel in this region so the actual sample number is low ?

Any help? Great many thanks
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