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UnifiedGenotyper miss some alleles while using GENOTYPE_GIVEN_ALLELES mode
Dear GATK team,
We are using UnifiedGenotyper GENOTYPE_GIVEN_ALLELES modes to do genotyping, but we found that not all given alleles were genotyped.
For example, the input vcf is:
13 20763485 . AG A 30 PASS AC=1;AF=0.500;AN=2;set=variant2 GT:GQ ./. 0/1:30 13 20763485 . A G 30 PASS AC=1;AF=0.500;AN=2;set=variant GT:GQ 0/1:30 ./.
in the output vcf, we only got genotypes:
13 20763485 rs80338943 AG A 0 LowQual AC=0;AF=0.00;AN=2;BaseQRankSum=1.075;DB;DP=820;ExcessHet=3.0103;FS=0.000;MLEAC=0;MLEAF=0.00;MQ=59.95;MQ0=0;MQRankSum=0.074;RPA=3,2;RU=G;ReadPosRankSum=1.087;SOR=1.546;STR GT:AD:DP:GQ:PL 0/0:819,1:820:99:0,2462,36389
another allele were missed
the command we used is:
java -jar GenomeAnalysisTK-3.6.jar -T UnifiedGenotyper -mbq 10 -stand_call_conf 20 -dt NONE -R hs37d5.fa -I S44-EL-20-1.recal.bam -D dbsnp147_GRCH37_All_20160601.vcf --genotyping_mode GENOTYPE_GIVEN_ALLELES --alleles input.vcf -L input.vcf -o output.vcf --output_mode EMIT_ALL_SITES
Is there any options we can make UnifiedGenotyper output all alleles?
Thanks a lot