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HaplotypeCaller filter option

my script:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R reference.fa -filterRNC -filterMBQ -filterNoBases -rf UnmappedRead -rf BadMate -rf DuplicateRead -rf NotPrimaryAlignment -rf MappingQualityUnavailable -recoverDanglingHeads -dontUseSoftClippedBases -stand_call_conf 20 -stand_emit_conf 20 -o WT.vcf -I WT.bam

there is some strange results in VCF, such as:
Unigene0001766 300 . T C 7075.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-3.715;ClippingRankSum=-0.042;DP=236;FS=5.542;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=0;MQRankSum=0.228;QD=29.98;ReadPosRankSum=-3.631 GT:AD:DP:GQ:PL **1/1:14,222**:236:99:7104,131,0

this is likely use default option to determin genotype, why not 0/1?
I didn`t see any options to control it.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    In its current implementation, the program expects diploid proportions by default, so such a skewed ratio can not be called 0/1 since it diverges too far from 50:50 ratio. If this is RNAseq and you think this could be a case of differential allele expression (which you would need a DNAseq control to support), then we may have a new tool in the next version that will be able to interpret this correctly. But it is not yet ready.

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