Hi Team,
I downloaded exome chromosome wise vcf file from: gs://gcp-public-data–gnomad/release/4.1/vcf/exomes/ and there is no “All chromosomes VCF” for this version.
Using these chromosome wise files i generated final vcf for 24 chromosomes. Then i try to run the “Mutect2” and getting following error: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0.
As per the some forum discussion (https://gatk.broadinstitute.org/hc/en-us/community/posts/25681424869787-Mutect2-Filtering-Discrepancy-with-Different-Versions-of-gnomAD-Germline-Data), I need to modify the the gnomAD vcf.
I am trying to run following command and to get the somatic variants:
gatk Mutect2 --native-pair-hmm-threads 60 -R hg38.fa --intervals File.bed --lenient true --max-population-af 0.01 --min-base-quality-score 20 --germline-resource gnomad.exomes.v4.1.sites.All_24chr_Final.vcf.gz -I SampleID.bam -O SampleID.Mutect2-gnomAD.vcf --java-options -Xmx100g
Please help me some one on this issue and Thanks in advance.