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Picard 2.10.2 is now available. As of 2.10.0, Picard supports NovaSeq CBCL data. Download and read release notes at https://github.com/broadinstitute/picard/releases.
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Read-Backed phasing and Indels

NadiaNadia Member
edited August 2013 in Ask the GATK team

Hi,
I'm calling Haplotypes of a diploid genome with the HaplotypeCaller and using the Read-Backed Phasing tool afterwards. I believe that Indels can't be phased so far. My output files look like the example showed below. In the example below there is an Indel at Position 795. As you can see, the alternative alleles in position 779 and 787 belong to the same haplotype. Do the alternative alleles in position 799 and 805 also belong to that haplotype or do I only have the phasing information for regions between the Indels and have to find another method to get a continuous sequence for each haplotype? Can I also assume that that haplotype which has the "C" in position 779 and "T" in position 787 has a Deletion (of AAA) in position 795?

GSVIVT01012049001 779 . A C 5696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;ClippingRankSum=0.538;DP=272;FS=4.894;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.499;QD=20.94;ReadPosRankSum=0.640 GT:AD:DP:GQ:PL:PQ 0|1:121,147:268:99:5725,0,11316:10524.93

GSVIVT01012049001 787 . A T 5671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.203;ClippingRankSum=0.297;DP=259;FS=1.517;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.090;QD=21.90;ReadPosRankSum=0.815 GT:AD:DP:GQ:PL:PQ 0|1:117,139:256:99:5700,0,11316:10067.97

GSVIVT01012049001 795 . TAAA T 2147483609.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.922;ClippingRankSum=-0.641;DP=254;FS=1.014;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.316;QD=27.70;ReadPosRankSum=1.731 GT:AD:DP:GQ:PL 0/1:114,131:245:99:5024,0,15611

GSVIVT01012049001 796 . A T 3273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.717;ClippingRankSum=0.329;DP=245;FS=1.005;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.631;QD=13.36;ReadPosRankSum=-1.317 GT:AD:DP:GQ:PL:PQ 1|0:126,111:237:99:3302,0,11019:3862.78

GSVIVT01012049001 799 . A T 3554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.422;ClippingRankSum=-0.037;DP=244;FS=0.483;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.095;QD=14.57;ReadPosRankSum=0.600 GT:AD:DP:GQ:PL:PQ 0|1:111,118:229:99:3583,0,16191:3906.37

GSVIVT01012049001 805 . G A 4959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.604;ClippingRankSum=1.035;DP=237;FS=2.951;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=1.228;QD=20.93;ReadPosRankSum=-0.923 GT:AD:DP:GQ:PL:PQ 0|1:99,134:233:99:4988,0,9612:8723.87

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