Missing AC, AN, Af tagsin vcf files genrated with HaplotypeCaller/ GenotypeGVCFs

Following the the recommended best practice and using GATK v3.2, the raw vcf file created by haplotyecaller/GenotypeGVCFs does not contain any of AC, AN and AF tags. Is this an expected behaviour?

This is a line of the g.vcf file generated from HaplotypeCaller:
chr21 36104982 . AT A,ATT,<NON_REF> 0.39 . BaseQRankSum=-1.693;DP=35;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQ=60.00;MQ0=0;MQRankSum=1.874;ReadPosRankSum=-0.023 GT:AD:GQ:PL:SB 0/1:23,6,2,0:27:27,0,499,67,411,529,96,459,496,525:10,13,2,4

And the raw vcf file from GenotypeGVCFs: chr21 36122885 . A AT 7871.94 . BaseQRankSum=0.151;DP=493;FS=5.433;MLEAC=24;MLEAF=0.750;MQ=60.00;MQ0=0;MQRankSum=0.129;QD=19.53;ReadPosRankSum=0.257 GT:AD:DP:GQ:PL 0/1:13,8:.:99:162,0,238 1/1:0,21:.:62:536,62,0 1/1:0,24:.:71:610,71,0 0/1:12,12:.:99:245,0,207 1/1:0,27:.:80:693,80,0 1/1:0,34:.:99:877,101,0 0/1:31,13:.:99:210,0,624 0/0:30,0:30:65:0,65,1125 0/1:6,11:.:96:225,0,96 0/1:10,5:.:87:87,0,196 0/1:4,15:.:39:340,0,39 1/1:2,35:.:66:895,66,0 1/1:0,53:.:99:1376,161,0 1/1:0,13:.:39:328,39,0 1/1:0,24:.:74:662,74,0 1/1:1,29:.:65:702,65,0

My command for HaplotypeCaller:
java -Xmx8g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R myRef.fa -I my.bam -L chr21 --dbsnp dbSNP_chr21.vcf --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -stand_emit_conf 10 -stand_call_conf 30 -mbq 20 -nct 8 -A FisherStrand -A QualByDepth -A HaplotypeScore --annotation Coverage -o raw.g.vcf

And GenotypeGVCFs:
java -Xmx8g -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R myRef.fa -V myVCF.list --dbsnp dbSNP_chr21.vcf -A FisherStrand -A QualByDepth -A HaplotypeScore -A Coverage -L chr21 -o myraw.vcf

Answers

Sign In or Register to comment.