Hey,

I am trying to filter my VCF that come from the Mutect2 calling command, the best way possible. I have a lot of trouble creating my own PON because of GenomicsDBImport error : GenomicsDBImport does not support GVCFs with MNPs. I am trying to use another parameter in FilterMutectCalls command, which is contamination table, coupled with tumor segmentation. However, I have the same exact number of variants that PASS the filter, with or without adding contamination parameters :

1) pileups for tumor sample

gatk GetPileupSummaries \
     -I tumor_KTN102-2.bam \
     -V af-only-gnomad.hg38.vcf.gz \
     -L intervals.interval_list \
     -O grosse_commande_KTN102-2_pileups.table

2) pileups for blood sample

gatk GetPileupSummaries \
     -I blood_KTN102-b.bam \
     -V ../KTN102-2/af-only-gnomad.hg38.vcf.gz \
     -L intervals.interval_list \
     -O grosse_commande_KTN102-b_pileups.table

3) contamination

gatk CalculateContamination \
     -I grosse_commande_KTN102-2_pileups.table \
     -matched grosse_commande_KTN102-b_pileups.table \
     -O contamination.table \
     -tumor-segmentation tumor_segments.table

4) Filtering

gatk FilterMutectCalls \
     --contamination-table contamination.table\
     --tumor-segmentation tumor_segments.table \
     -V grosse_commande_KTN102-2.vcf \
     -O grosse_commande_KTN102-2_F.vcf \
     -R /home/sbesseau/scratch/LOTUS/genome.fa

GATK 4.1.2

Thank you