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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

VariantAnnotator not recognising QD annotations

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    Gökalp Çelik

    Hi Samuel Brown Araujo

    One thing that caught my attention is the presence of the below annotation in your input vcf file

    RAW_MQandDP

    This annotation is only present in the GVCF files and it is split and distributed to MQ and DP annotations in the final VCF. Could you be trying to recalibrate a GVCF file?

    Can you provide us a few vcf lines from that file?

    If it is indeed a GVCF file it must be genotyped by GenotypeGVCFs before you can recalibrate it. 

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    Samuel Brown Araujo

    Hi Gökalp Çelik

    I am working with VCF samples. Here are a few lines from the file.

    I am still getting the following error:

    A USER ERROR has occurred: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.

    Oddly, I am only getting this for my indel file after splitting, not my SNP file.

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    Gökalp Çelik

    Your INDELs all seem to have filters. Can you remove these filters and try once again? I am trying to recreate this issue in my own data but so far I am unable to replicate the problem. Can you also try with 4.6.0.0?

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    Samuel Brown Araujo

    Gökalp Çelik, I have tried without the filters and still get the same issue. I have noticed that in some of my samples the error I get is not related to QD, it is the following:

    A USER ERROR has occurred: Bad input: Found annotations with zero variance. They must be excluded before proceeding.


    Could this shed any light on what the issue could be?

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    Gökalp Çelik

    VQSR requires variety among the values to generate a model to filter good ones from bad ones however if values have very limited or no variance among them then that annotation must be removed from the VQSR. Log should have indications about which annotations to remove.

     

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