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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 0:43,0:43:990.00:0,1813 1:0,66:66:99:1:1.00:1143,0 0:38,0:38:990.00:0,1627 0:127,0:127:990.00:0,5248 0:42,0:42:990.00:0,1739 0:100,0:100:990.00:0,4166