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low GQ around Indels

sgoyalsgoyal San CarlosMember

I thought the low GQ around indel was fixed in v4, but i still see it. Here is the arguments and output i am getting.

gatk-4.1.3.0/gatk HaplotypeCaller -I test.bam -ERC BP_RESOLUTION -R hg19_v6.fasta --dont-use-soft-clipped-bases true -L vcfreg_decoy.bed -O test.g.vcf

20 13765933 . G . . . GT:AD:DP:GQ:PL 0/0:276,0:276:99:0,120,1800
20 13765934 . G . . . GT:AD:DP:GQ:PL 0/0:273,0:273:99:0,120,1800
20 13765935 . A . . . GT:AD:DP:GQ:PL 0/0:270,0:270:99:0,120,1800
20 13765936 . G . . . GT:AD:DP:GQ:PL 0/0:264,1:265:99:0,120,1800
20 13765937 . G . . . GT:AD:DP:GQ:PL 0/0:260,0:260:99:0,120,1800
20 13765938 . T . . . GT:AD:DP:GQ:PL 0/0:256,1:257:99:0,120,1800
20 13765939 . G . . . GT:AD:DP:GQ:PL 0/0:253,0:253:99:0,120,1800
20 13765940 . A . . . GT:AD:DP:GQ:PL 0/0:250,0:250:99:0,120,1800
20 13765941 . G . . . GT:AD:DP:GQ:PL 0/0:241,1:242:99:0,120,1800
20 13765942 . CCCGCGGGG C, 3998.60 . BaseQRankSum=0.112;DP=251;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.379;RAW_MQandDP=1219021,251;ReadPosRankSum=2.187 GT:AD:DP:GQ:PL:SB 0/1:112,121,0:233:99:4006,0,7937,4343,8306,12648:37,75,40,81
20 13765943 . C . . . GT:AD:DP:GQ:PL 0/0:114,121:235:0:0,0,0
20 13765944 . C . . . GT:AD:DP:GQ:PL 0/0:110,122:232:0:0,0,0
20 13765945 . G . . . GT:AD:DP:GQ:PL 0/0:107,121:228:0:0,0,0
20 13765946 . C . . . GT:AD:DP:GQ:PL 0/0:106,121:227:0:0,0,0

20 13767948 . A . . . GT:AD:DP:GQ:PL 0/0:223,0:223:99:0,120,1800
20 13767949 . A . . . GT:AD:DP:GQ:PL 0/0:221,0:221:99:0,120,1800
20 13767950 . T . . . GT:AD:DP:GQ:PL 0/0:220,0:220:99:0,120,1800
20 13767951 . C . . . GT:AD:DP:GQ:PL 0/0:226,0:226:99:0,120,1800
20 13767952 . C . . . GT:AD:DP:GQ:PL 0/0:230,0:230:99:0,120,1800
20 13767953 . T . . . GT:AD:DP:GQ:PL 0/0:228,0:228:99:0,120,1800
20 13767954 . T . . . GT:AD:DP:GQ:PL 0/0:221,2:223:99:0,120,1800
20 13767955 . C . . . GT:AD:DP:GQ:PL 0/0:223,0:223:99:0,120,1800
20 13767956 . A . . . GT:AD:DP:GQ:PL 0/0:231,0:231:99:0,120,1800

20 13767957 . G . . . GT:AD:DP:GQ:PL 0/0:230,0:230:99:0,120,1800

21 38269435 . T . . . GT:AD:DP:GQ:PL 0/0:237,0:237:99:0,120,1800
21 38269436 . G . . . GT:AD:DP:GQ:PL 0/0:236,0:236:99:0,120,1800
21 38269437 . T . . . GT:AD:DP:GQ:PL 0/0:237,0:237:99:0,120,1800
21 38269438 . C . . . GT:AD:DP:GQ:PL 0/0:240,0:240:99:0,120,1800
21 38269439 . A . . . GT:AD:DP:GQ:PL 0/0:240,0:240:99:0,120,1800
21 38269440 . T . . . GT:AD:DP:GQ:PL 0/0:233,0:233:99:0,120,1800
21 38269441 . A . . . GT:AD:DP:GQ:PL 0/0:231,0:231:99:0,120,1800
21 38302541 . C . . . GT:AD:DP:GQ:PL 0/0:166,0:166:99:0,120,1800
21 38302542 . A . . . GT:AD:DP:GQ:PL 0/0:164,0:164:99:0,120,1800
21 38302543 . CA C, 2094.60 . BaseQRankSum=-0.678;DP=169;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.762;RAW_MQandDP=821338,169;ReadPosRankSum=0.653 GT:AD:DP:GQ:PL:SB 0/1:86,69,0:155:99:2102,0,2723,2361,2932,5292:66,20,56,13
21 38302544 . A . . . GT:AD:DP:GQ:PL 0/0:90,70:160:0:0,0,640
21 38302545 . A . . . GT:AD:DP:GQ:PL 0/0:162,0:162:99:0,120,1800
21 38302546 . C . . . GT:AD:DP:GQ:PL 0/0:166,0:166:99:0,120,1800
21 38302547 . T . . . GT:AD:DP:GQ:PL 0/0:171,0:171:99:0,120,1800
21 38302548 . C . . . GT:AD:DP:GQ:PL 0/0:173,0:173:99:0,120,1800
21 38302549 . A . . . GT:AD:DP:GQ:PL 0/0:176,0:176:99:0,120,1800
21 38302550 . C . . . GT:AD:DP:GQ:PL 0/0:178,0:178:99:0,120,1800
21 38302551 . C . . . GT:AD:DP:GQ:PL 0/0:180,0:180:99:0,120,1800
21 38302552 . T . . . GT:AD:DP:GQ:PL 0/0:180,0:180:99:0,120,1800
21 38302553 . C . . . GT:AD:DP:GQ:PL 0/0:179,0:179:99:0,120,1800
21 38302554 . C . . . GT:AD:DP:GQ:PL 0/0:178,1:179:99:0,120,1800

Answers

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