Hi,
I am looking to use HaplotypeCaller to call germline variants, and I am particularly interested in the orientation of these variants relative to one another (cis- or trans-). There seems to be reference to physical phasing in the (HaplotypeCaller documentation)[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_haplotypecaller_HaplotypeCaller.php#--do-not-run-physical-phasing], but I cannot find any physical phasing information in my VCF file.
For instance, I would expect the two variants below:
1 1647722 . G T 307.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.861;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.28;MQRankSum=-5.260;QD=10.61;ReadPosRankSum=-0.098;SOR=0.155 GT:AD:DP:GQ:PL 0/1:21,8:29:99:315,0,841
1 1647725 . G A 304.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.38;MQRankSum=-5.262;QD=10.50;ReadPosRankSum=-0.448;SOR=0.204 GT:AD:DP:GQ:PL 0/1:20,9:29:99:312,0,883
to be in the cis- orientation because they share nearly identical read counts, but I cannot find a corresponding annotation in the VCF file that says as much.
My command to call HaplotypeCaller is as below:
$gatk_launcher --java-options -Xmx${mem}g HaplotypeCaller \
-R $reference \
-I $bam_file \
-O $out_file \
-L $intervals_split &>> $log_file
Thank you for the help!!