variant calling
2
0
Entering edit mode
13 days ago
Elisa • 0

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.

mutect2 • 297 views
0
Entering edit mode
6 days ago
g.papp-co ▴ 10

Hi!

You can use Mutect2 with tumor only mode using a PoN and germline resource.

Consider filtering as well, but from what i have read from others, the whole tumor-only procedure is not advisable.

0
Entering edit mode

It is not really clear to me how to build or where to find PoN and a germline resource.

0
Entering edit mode

0
Entering edit mode
6 days ago

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 \
--vcf freebayes_PIK3CA.vcf ;


Obviously there are limitations to the results produced.

Kevin