Dear GATK Team,
Here is a record in my gvcf file
chr1 14726 . T <NON_REF> . . END=14730 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,15
I generated this by the following command:
gatk --java-options "-Xmx4g" HaplotypeCaller -R GRCh38.primary_assembly.genome.fa -I "$input_file" -O "$output_file" -ERC GVCF
I think it means that there is no variant between chr1:14726 and chr1:14730. However, I am not sure if I could believe GT, DP, GQ, MIN_DP, PL of all the five sites (14726-14730) are all 0/0:1:3:1:0,3,15.
If not, how can I get the INFO of these five sites except setting ERC to BP_RESOLUTION? Is that the only choice?
Thank you for any help you can provide.
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