How to interpret INFO part of non-variant blocks in gvcf files?Answered
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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Hi Jiayi Zhao,
I believe the question you are asking is regarding the GT, DP, GQ, MIN_DP, PL information. These are actually genotype fields and not INFO fields. Here is an article about the GVCF format: https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-GVCF-Genomic-Variant-Call-Format.
You are correct that there is no variant in any of these five sites. The only way to get site-level genotype information would be run HaplotypeCaller in ERC BP_RESOLUTION mode, as you said. Reference blocks save a lot of resources which is why we generally recommend -ERC GVCF mode and not BP_RESOLUTION.
The PL and GQ are helpful here in determining confidence of this reference block. The PL is only 15 and the GQ is only 3. The GQ is the reference confidence score. It is very low here because there is only 1 read supporting these sites. I don't believe that you would get much more information if you were to run HaplotypeCaller in BP_RESOLUTION mode and inspect these sites.
Please let me know if you have any more questions.
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