Are there any repository for panel of normal for running Mutect2?
0
2
Entering edit mode
3.2 years ago
DareDevil ★ 4.3k

I am trying to call somatic mutations from tumor sample where I don't have any normal sample. Are there any repository for panel of normal or a downloadable file like pon.vcf.gz

gatk4_mutect2_4136_pon.vcf.gz

I want to run

gatk Mutect2 -R hg38.fa \
-I input_tumor.bam \
-pon gatk4_mutect2_4136_pon.vcf.gz \
--germline-resource af-only-gnomad.hg38.vcf.gz \
--af-of-alleles-not-in-resource 0.0000025 \
--genotype-germline-sites \
-L exome_autoXYM.intervals \
-O mt2_unmatched.vcf.gz
Mutect2 PON panel of normal gatk • 1.2k views
ADD COMMENT
2
Entering edit mode

Publicly Available WGS Samples for Panel of Normals? and many other threads, please use the search function before posting.

ADD REPLY

Login before adding your answer.

Traffic: 1789 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6