Hi everyone,
I must perform somatic variant calling on ovarian samples (targeted sequencing performed with Illumina). I do not have the control match; it is still correct to use Mutect2 or do you have any other tool to suggest me ? Moreover, I'd like to know if I should perform local realignment around indels.
Thanks in advance
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written
by
Elisa •
2 answers
Hi!
You can use Mutect2 with tumor only mode using a PoN and germline resource.
https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2
Consider filtering as well, but from what i have read from others, the whole tumor-only procedure is not advisable.
As for the realignment, i think's it's not neccesary anymore but please read: https://gatk.broadinstitute.org/hc/en-us pipeline part.
Germline resources can be downloaded from https://gnomad.broadinstitute.org/ website as a google cloud public datasets. I have never used PoN but there is a little article about it: https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON- and also some download links.
freebayes can do this, too, and it's easy to specify genomic intervals. For example:
freebayes \
--region chr3:178148114-180240093 \
--fasta-reference ref_genome.fa \
--bam reheader.bam \
--vcf freebayes_PIK3CA.vcf ;
Obviously there are limitations to the results produced.
Kevin
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