Hi,
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
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, Alva