I have an issue that I'm not sure how to solve. I'm using HaplotypeCaller with a three member family and I have some calls when the HOM/HET call doesn't match with what we expected:
chr1 94487191 . A T 93.13 . AC=1;AF=0.167;AN=6;BaseQRankSum=-0.540;ClippingRankSum=-0.374;DP=87;FS=4.946;MLEAC=1;MLEAF=0.167;MQ=61.11;MQ0=0;MQRankSum=-0.042;QD=7.16;ReadPosRankSum=-0.042;set=GATK GT:AD:GQ:PL 0/0:40,0:99:0,102,2405 0/0:33,0:90:0,90,2215 0/1:11,2:99:124,0,760
In the third sample, the call is 0/1 (HET) but the coverage of each allele is 11 and 2, that means, with just 18% is considered as HET. There is a way to change the Allele Balance to 30%?
The Genome Analysis Toolkit (GATK) v2.5-2-gf57256b, Compiled 2013/05/01 09:27:02
Program Args: -T HaplotypeCaller -R ucsc.hg19.fasta -I S1.bam -I S2.bam -I S3.bam -o OUT.RAW.vcf --genotyping_mode DISCOVERY -stand_call_conf 30.0 -stand_emit_conf 10.0