Creating a GenomicsDBImport from the normal Mutect2 calls

Question

[s.awasthy]

Hello all, I am working on exome-seq data of 30 samples(tumor and matched normal) and using gatk-4.1.1.0 for the analysis of somatic mutations but got stuck in the second step of creation of panel of Normals. I am using a bed file provided by sequencing company(10MB) as an interval list file but it's taking too much time for running and space too.. and end up with error: **GenomicsDBConfigException : Syntax error in JSON file Please suggest me how can i resolve it?

[curious]

Hey could you provide some more detail on what you are actually doing. I have been working with GATK for the last couple days including the GenomicsDBImport utility.

[s.awasthy]

Hello Sir, I need to identify somatic mutations from exome-seq data and for that purpose panel of Normals need to be created from all the normal samples of my study. For reference, i have attached the link of protocol which i am following https://gatk.broadinstitute.org/hc/en-us/articles/360035531132?id=24057

[curious]

There is another command to combine gvcfs, I used that instead of making a db, but in the end I didn't need a db. I dont know if a workaround is possible

What is your actual command and what version are you running. I did get the db to be made successfully

[s.awasthy]

Hello Sir, My actual command is: gatk GenomicsDBImport -R reference.fasta -L intervals.interval_list \ --genomicsdb-workspace-path pon_db \ -V normal1.vcf.gz \ -V normal2.vcf.gz \ -V normal3.vcf.gz i am using GATK 4.1.1.0.

Answer 1

[s.awasthy]

After searching through various discussion forums of GATK finally I am able to resolve the query. By adding --merge-input-intervals option to above command will resolve the error.