Filtering VCF files

Question

[chrisgr]

Hi,

I managed to align some fastq files and got to the point of raw VCF files. Now I would like to filter them based on some filters using gatk VariantFiltration. But I'm completely stuck and overwhelmed on what to filter on. As I'm new to filtering VCF's I hoped to find some default values that most people use.

I've found a post What are good settings for filtering VCF files? which seemed very helpful providing some filters. But I am having a very hard time figuring out how to use these filters in VariantFiltration or even providing this information in my VCF with Haplotypecaller.

For instance: "BaseQualBias" nowhere in the manuals of HaplotypeCaller or VariantFiltration is this even mentioned. I've tried looking for keywords of "bias", "quality bias". How do people use these kind of tools?

Same with MinMQ, nowhere I can find anything about RMS root mean square quality or anything that comes close to it.

I'm a bit overwhelmed, what would be the best to do here?

Thanks in advance!

Answer 1

[Pierre Lindenbaum]

I can find anything about RMS root mean square quality

https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants

This is the root mean square mapping quality over all the reads at the site. Instead of the average mapping quality of the site, this annotation gives the square root of the average of the squares of the mapping qualities at the site.

[chrisgr]

Thank you for your reponse! Sorry what I meant was that I cant find how to filter on that using VariantFiltration tool, nothing in the manual about it. I did find how to include this RMS value in my VCF file but then how do I determine if it is worth to even filter on? (I am now n doubt because this value isn't provided as default value, so I guess it's not important enough?)