Confusing GVCF results

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Yue Wang

• July 07, 2020 14:31
• Edited

Hi,

I am working on a haploid fungus and used GATK 4.1.7 HaplotypeCaller to call variants following the BQSR pipeline. After that, I used bcftools to merge the gvcf files followed this command:

gatk-4.1.7.0/gatk --java-options "-Xmx4g" GenotypeGVCFs -R ../../B8441.fa -V Merge.snp.gvcf -O Merge.snp.gt.gvcf

When I checked my results. I got some loci like this 

1. I know .:0,0 means no calls were made at that position for that sample. Does that mean I could use the reference allele for that sample? 

2. What does .:204,0:204 in position 30158 mean? It seems that the read depth for the ref (A) is 204 and for the alt (T) is 0. However when I go back to check the recal_reads.bam file for that sample, it looks like this sample has some alt (T) allele in position 30158. Could you clarify this?

 Thank you very much!

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  Genevieve Brandt (she/her)

  • July 23, 2020 21:13

  Hi Yue Wang,

  Please see this: https://gatk.broadinstitute.org/hc/en-us/articles/360035891111-Expected-variant-at-a-specific-site-was-not-called#:~:text=This%20can%20happen%20when%20you,be%20missing%20a%20real%20variant.

  And this: https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant

  For information about why certain variants are called. The algorithms are complex, but call most variants that have enough evidence. 

  Also, just in case your methods are leading to any problems, here is our best practices pipeline: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-. We recommend GenomicsDBImport to consolidate the GCVFs. 

   

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