Entering edit mode
8 months ago
Samuel
▴
20
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