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Missing reference allele in GVCF file after running HaplotypeCaller
I used HaplotypeCaller in GVCF mode to generate a single sample GVCF, but when I checked my vcf file I see that the reference allele is not showing up:
22 1 . N <NON_REF> . . END=16050022 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 22 16050023 . C <NON_REF> . . END=16050023 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,37 22 16050024 . A <NON_REF> . . END=16050026 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,73 22 16050027 . A <NON_REF> . . END=16050035 GT:DP:GQ:MIN_DP:PL 0/0:3:9:3:0,9,110 22 16050036 . A C,<NON_REF> 26.80 . BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;MLEAC=1,0;MLEAF=0.500,0.00;MQ=27.00;MQ0=0;MQRankSum=-0.736;ReadPosRankSum=0.736 GT:AD:DP:GQ:PL:SB 0/1:1,2,0:3:23:55,0,23,58,29,86:1,0,2,0 22 16050037 . G <NON_REF> . . END=16050037 GT:DP:GQ:MIN_DP:PL 0/0:3:9:3:0,9,109 22 16050038 . A <NON_REF> . . END=16050039 GT:DP:GQ:MIN_DP:PL 0/0:4:12:4:0,12,153
I am not sure where to start troubleshooting for this, since all the steps prior to using HaplotypeCaller did not generate any obvious errors.
The basic command that I used was:
java -Xmx4g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R hs37d5.fa -I recal_1.bam -o raw_1.vcf -L 22 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000
Have you encountered this problem before? Where should I start troubleshooting?
Thanks very much in advance,