Mutect2 --artifact_detection_mode for tumor-only calling : can i use PoN
I am aware that "Tumor-only variant calling is possible but it is not supported with Mutect2".
Thing is, i am working on a study with few normals.
I did create my PoN with the 10 available normals.
I am planning on calling the 10 tumor-normal pairs as planned with Mutect2.
For the remaining "tumor-only" samples, the plan is to use --artifact_detection_mode :
java -jar $GATK -T MuTect2 -nct 8 \ -R ucsc.hg19.fasta \ -I:tumor tumor.bam \ --dbsnp dbsnp_138.hg19.vcf \ --cosmic cosmic_coding_and_noncoding_chr_M_sorted.vcf \ -L targets.interval_list \ --artifact_detection_mode \ -o out_artifactmode.vcf
I was wondering if i could use the -PON argument alongside with --artifact_detection_mode ?
I know it feels counter-intuitive, given that the --artifact_detection_mode is primary designed to build the PoN.
java -jar $GATK -T MuTect2 -nct 8 \ ... \ -PON pon.vcf \ --artifact_detection_mode \ ... \
If it's not possible, i guess i will then use the PoN as one of the many filters in the post-processing steps on those "out_artifactmode.vcf"
Best regards, Erwan