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No coverage information for some sites after BP RESOLUTION haplotype caller?

Dear GATK team,

We are trying to run GATK haplotype caller with BP RESOLUTION to get coverage information for each site. But it seems like some sites don't have any cov information, for example:
jcf7180012625382:4560 4560 . A G, 0.01 . MLEAC=0,0;MLEAF=NaN,NaN GT ./.

I wonder if it is because GATK is not sure about how to call this SNP because signal is too low, or there are some explanations can help me with this issue?

Thank you for the help!

Best,
Yuanwen

Answers

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @yuanwen
    Would you be able to post the command that you used and the version that you are using to get this output?It does look like the QUAL score of this site is quite low which might be a reason that you are not able to see coverage information but more details of how you arrived at this record will help!

  • yuanwenyuanwen Member

    Thank you for helping me with this issue!

    Sure, the command I am using is:
    gatk --java-options "-Xmx70g" HaplotypeCaller -R masked_genome.fasta -I input.bam -O output.g.vcf.gz -ERC BP_RESOLUTION

    I used version gatk-4.0.12.0 to get this output.

    Much appreciated,
    Yuanwen

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @yuanwen

    Sorry for the delay but we are looking into it and will get back to you soon!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @yuanwen It looks like you have used a masked_genome.fasta file which might be resulting in the missing bases of coverage. In general, a masked reference genome's repetitive parts are hidden away (turned into n's), so they won't be aligned to. If you could try again with a reference genome that is unmasked you will probably be able to see the missing base coverages.

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