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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

QUAL scores being returned as "." in output from CombineGVCFs

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    Gökalp Çelik

    Hi Utpal Smart

    When GVCF files are combined to create a multisample GVCF file certain parameters are removed for future recalculation and recalculating those parameters require GenotypeGVCFs tool to run on your combined file. When you run the tool to get genotyped sites in a regular multisample VCF you will get your qual values as well as calls in regular spots. 

    The behavior you observe is the normal behavior of our tools. 

    I hope this helps. 

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    Utpal Smart

    Hi Gökalp Çelik 

    Thanks for that response. So, if wanted to filter variants by qual scores, I would do it after running GenotypeVCFs on the combined gvcf first? 

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    Gökalp Çelik

    Hi again.

    Yes exactly. You need to run GenotypeGVCFs first to get your genotypes and scores calculated. Then you may use whatever filtering tool to cleanup your variants. 

    Regards. 

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    Utpal Smart

    Perfect, thank you for that prompt clarification. One last related question: does the "WARN  IntelInflater - Zero Bytes Written: 0" in the output indicate issues with combining gvcfs? I can open a new post about this if that is more appropriate.

    Thanks.

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    Gökalp Çelik

    That warning is not an error message. It is the regular behavior of the tool indicating that there were zero instances where tool was used to write 0 bytes as output. It will not affect your results and your output should be ok. 

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    Utpal Smart

    Good to know and thank you for those answers Gökalp Çelik 

    Regards,

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