Germline Variants Calling
This is no error or issue, this is a question on how I could subtract the variants called in the tumour samples against the ones of the control samples (as background), using the results of HaplotypeCaller. I'm already using Mutect2 also, but I know HC detects some variants that mutect2 does not, and the same other way around. How could I perform that "subtraction"?
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This is can actually be performed in a single step using the control samples as normal in your tumor callings. Mutect2 and HaplotypeCaller share the same variant calling engine with the exception of Mutect2 being more sensitive than HaplotypeCaller therefore it may call anything that HaplotypeCaller can call in a germline sample. Once a normal and tumor file is provided with normal sample name to Mutect2 it can detect all variants and provide proper flags for FilterMutectCalls tool to mark germline variants as Germline in the filter column and mark anything that passes to be somatic as PASS in the final VCF.
I hope this helps.
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And could I ask you, for annotating variants can I use snpEFF tool on the output of Mutect2? Or do you recommend GATK VariantAnnotator?
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VariantAnnotator is not what you expect it to be. VariantAnnotator is used to annotate variants with parameters picked from reads, variants, samples to extend the information about the variant call itself. It may utilize external sources to add more data however it is not meant to be used for functional annotation.
You may want to check Funcotator, VEP and others to do that.
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Could I apply funcotator to mouse samples? And which databases would I need?
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Unfortunately we do not have pre-made mouse resources for Funcotator. I would suggest you pick SnpEFF or VEP for this purpose.
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