Mutect2 PON VCF
a) GATK version used: 4-4.1.4.1-0
b) Exact command used: gatk Mutect2 -R /home/refererence/GRCh38PicardIDX/GRCh38.p12_genomic.fa -I /home/NewExomeBC2020/sorted_RBRN02_Dedup.bam -tumor RBRN02 --germline-resource /home/GATK-RefFiles/somatic-hg38_af-only-gnomad.hg38.vcf.gz -O /home/NewExomeBC2020/RefVCFs/RBRN01.vcf.gz
c) Entire error log: A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.
I understand this problem happen due to incompatibility of Ref. Genome used for alingmnet and The VCF provided by GATK(whihc actually have UCSC contigs).
d) Where do I find compatible VCF for GRCh38 gencode Reference?
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Thanks for your contribution woodword!
avrajit were you able to solve this issue? Your question was posted while our GATK Team was Out of Office and we did not get to your question.
If you still would like support from the GATK Team, please repost your question with [Repost] in the title and we will get to it as soon as possible.
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I found GATK references follow ucsc hg38. Coding. Using ucsc hg38 can solve the problem. I did the same. Thanks
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