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

Join Date: Feb 2013
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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 -
PASS
VQSRTranchesSNP (with various percentiles)
IndelFS
IndelQD

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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