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Possible bug in variant filtering?
I was pulling my hair out over this one.
I was applying a hard filter to a genotyped gVCF using JEXL to access variant context attributes to decide what filter setting I would apply. The filter was
"vc.getGenotype("%sample%").isHomRef() ? vc.getGenotype("%sample%").getAD().size() == 1 ? DP < 10 : ( DP - MQ0 ) < 10 or ( MQ0 - (1.0 * DP) ) >= 0.1 or MQRankSum <= 3.2905 or ReadPosRankSum >= 3.2905 or BaseQRankSum >= 2.81 : false"
In pseudocode it says:
`if ( isHomRef ) then if ( getAD().size() == 1 ) then DP < 10 else ( DP - MQ0 ) < 10 or ( MQ0 - (1.0 * DP) ) >= 0.1 or MQRankSum >= 3.2905 or ReadPosRankSum >= 3.2905 or BaseQRankSum >= 2.81 else ignore record`
The idea being that for records where not all reads contained the reference allele, we would filter out those positions where there was evidence to suggest that the reads supporting an alternate allele were of a significantly better quality. However, running this filter I keep getting the warning (snipped for clarity):
WARN [SNIP]... MQRankSum <= 3.2905 [SNIP]... : false;' undefined variable MQRankSum
So I thought the filter was failing. However, just as a test, I changed the direction of
<=3.2905 (a bit nonsensical, it should basically apply the filter to almost all
HomRef positions that had any reads supporting an alternate allele).
I still get the warning but I found the filter was applied to variant records as it should be. e.g. the following went from
Supercontig_1.1 87 . C A . BAD_HOMREF BaseQRankSum=2.79;DP=40;MQ=39.95;MQ0=0;MQRankSum=-2.710e+00;ReadPosRankSum=0.819;VariantType=SNP GT:AB:AD:DP 0/0:0.870:34,5:39
So the filter is being correctly applied, but I am not sure why all the warnings are being generated? Is this a bug? Have I done something wrong?