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GT:AD:DP:GQ:PL instead of GT:DP:GQ when merging two vcf files with more than two alleles
Hi I have two vcf files, each with the same chr:pos, but alleles are different:
$ tail -1 test1.snp.vcf
chr17 41267926 . G A 50.77 . xxx GT:AD:DP:GQ:P 0/1:2,3:6:49:79,0,49
$ tail -1 test2.snp.vcf
chr17 41267926 . G C 15.88 LowQual xxx GT:AD:DP:GQ:P 0/1:3,2:6:44:44,0,85
After running CombineVariants below
$ java -jar GenomeAnalysisTK.jar -T CombineVariants -R ucsc.hg19.fasta -V test1.snp.vcf -V test2.snp.vcf -o ThreeAlleles.snp.vcf -genotypeMergeOptions UNIQUIFY
The ThreeAlleles.snp.vcf only have GT:DP:GQ instead of GT:AD:DP:GQ:PL in the FORMAT field
$ tail -1 ThreeAlleles.snp.vcf
chr17 41267926 . G A,C 50.77 PASS xxx GT:DP:GQ 0/1:6:49 0/2:6:44
How can I retain the GT:AD:DP:GQ:PL format for tri-allelic positions?