I am using Parabrick to extract somatic mutations in WES data while giving the following command, I am getting an error of Unknown argument specified "-pon".
The command and the arguments are as follows:
pbrun mutectcaller --ref ucsc.hg19.fasta \
--out-vcf subject1.vcf.gz \
--in-tumor-bam subject_tumor_bqsr.bam \
--in-normal-bam subject_normal_bqsr.bam \
--in-tumor-recal-file subject_tumor_recal.txt \
--in-normal-recal-file subject_normal_recal.txt \
--interval-file hglift_genome1.bed \
--mutectcaller-options="-pon /scratch/vivekr/pon1.vcf.gz \
--callable-depth 5 --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter \
--germline-resource /scratch/vivekr/refs/gnomad.exomes.r2.1.1.sites.vcf.bgz \
--enable-all-annotations true" \
--tumor-name subject_tumor \
--normal-name subject_normal \
--num-gpus 1
With the above command, I am passing an addtional supported mutect2 arguments like panel of normal, allow all possible annotations etc. But this is not working and getting an error of Unknown argument specified. Kindly suggest. Thanks.