Using Mutect 2 - question about Germline var, and PON
Hi,
I am aiming to use Mutect2, I see that it requires a germline-resource. I see one on the google bucket that is from 2017 - is there a newer one?
Further my mapped bam, have NCBI annotations, currently I have a script that changes the "chr1" type annotations into that used by NCBI of the form NC_000001.11 . I use this to convert the annotations of the PON (panel of normals) that I found on the google bucket, and I presume I'll have to use this as well for the germline-resource vcf, but first, I want to ask if this is a valid approach? Mapping the names shouldn't change anything down the line? And secondly, is there a panel of normals, and germline-resource already with the same annotations as the NCBI format?
Thank you!
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Our resource repositories contain the latest that we recommend therefore what you see there is what we recommend using. Also we recommend using reference genomes that we included in those resource bundles. We do not have any other resource files with NCBI id annotations.
In your case if you don't have resources to redo all mapping and variant calling steps using a reference genome we recommend you need to create your own germline resource vcf by replacing contig names but it is at your own risk to ensure the compatibility of the reference genome you use and germline resource that you will obtain after changing contig names. Keep in mind that downstream tools such as annotation tools may not like this approach and may require contig names to be as chr1,chr2 etc such as Funcotator.
Regards.
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