Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Follow up to EMIT_ALL_CONFIDENT_SITES

ProtaeusProtaeus Posts: 17Member
edited September 2012 in Ask the team

Hi,

I previously reported an issue in which I could not emit all sites or all confident sites when using a ploidy of 1. I downloaded the most recent version and it seems to be able to print the reference calls in these modes. The odd thing is that the quality for all those calls is the same and really low, which I know isn't a reflection of reality in all cases given the knowledge we have about the sequence data and its relationship to the reference. It is also consistent across many samples, whether I run multiple samples through a single GATK run or a single sample on its own. I pasted in an example from a recent run (multiple samples in same run). The problem is that all of these reference calls get a LowQual filter, which makes it difficult to differentiate from good LowQual calls. Any thoughts as to if this is to be expected and why that might be?

Reference   72  .   T   .   3   LowQual DP=281;MQ=50.69;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   187 .   T   .   3   LowQual DP=301;MQ=51.00;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   188 .   C   .   3   LowQual DP=296;MQ=50.84;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   206 .   A   .   3   LowQual DP=292;MQ=50.14;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   1844    .   T   .   3   LowQual DP=369;MQ=58.59;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   1854    .   C   .   3   LowQual DP=363;MQ=58.63;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   1972    .   A   .   3   LowQual DP=345;MQ=59.11;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   1993    .   T   .   3   LowQual DP=355;MQ=58.54;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   2096    .   C   .   3   LowQual DP=355;MQ=58.92;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   2376    .   T   C   1105.23 .   AC=1;AF=0.167;AN=6;BaseQRankSum=-10.910;DP=417;Dels=0.00;FS=27.994;HaplotypeScore=1.6883;MLEAC=1;MLEAF=0.167;MQ=58.90;MQ0=0;MQRankSum=0.195;NDA=1;QD=16.75;ReadPosRankSum=-5.021;SB=-4.370e+02;Samples=Ba-4599_4    GT:AD:DP:GQ:MLPSAC:MLPSAF:PL    0:43,0:43:99:0:0.00:0,1813  1:0,66:66:99:1:1.00:1143,0  0:38,0:38:99:0:0.00:0,1627  0:127,0:127:99:0:0.00:0,5248    0:42,0:42:99:0:0.00:0,1739  0:100,0:100:99:0:0.00:0,4166

Thanks, John

Post edited by Geraldine_VdAuwera on

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