How to interpret INFO part of non-variant blocks in gvcf files?

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Jiayi Zhao

• July 19, 2022 17:56

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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  Anthony DiCi

  • July 21, 2022 13:15

  Thank you for your post, Jiayi Zhao ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

   

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  Genevieve Brandt (she/her)

  • September 28, 2022 17:27

  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. 

  Best,

  Genevieve

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  Genevieve Brandt (she/her)

  • October 05, 2022 16:31

  Hi Jiayi,

  We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!

  Kind regards,

  Genevieve​

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