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Variant in sample gVCF missing when using GenotypeGVCFs to create a multi-sample VCF.
Hope you can me with an issue.
I have created a number of samples GVCF files using HaplotypeCaller and in one of the sample there is a variant in the GVCF file.
This is the variant in the sample GVCF:
chr17 62594511 . C A, 4.61 . BaseQRankSum=-1.380;DP=6;MLEAC=1,0;MLEAF=0.500,0.00;MQ=60.00;MQ0=0;MQRankSum=1.380;ReadPosRankSum=-1.380 GT:AD:GQ:PL:SB 0/1:4,2,0:31:31,0,146,43,152,195:4,0,1,1
When I run GenotypeGVFs to create the multiple samples VCF, I cannot find this variant in the output file. I believe I have setup the parameters to allow for the this variant to be picked up.
This is the instruction I'm using:
java -Djava.io.tmpdir=$TMPDIR -Xmx50g -jar /$GATK_DIR/GenomeAnalysisTK.jar -R $REFGENOME -T GenotypeGVCFs -V $GVCF_LIST -L $CHROM -o $FILE_NAME -stand_call_conf 30.0 -stand_emit_conf 0.0 --max_alternate_alleles 12 -nt 2
I hope you can help me in understanding why the variant from the GVCF was not passed on with the GenotypeGVCF call. It is very possible my call to GenotypeGVFs could be incorrect.