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Mutect2 with lastest nightly build problem
I am trying to run the variant calling step for the first time as a test. As I don't have any matched normal, I have only my tumour .bam file and a PoN composed of only 2 samples (for now).
So I combined my two .vcf normals to create a PoN and a launched MuTect2 like that :
java -jar /analysis/GATK/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar \
-T MuTect2 \
-R /projects/acoudray/star/ref_genome/hg38_gatk/GRCh38.primary_assembly.genome.fa \
-I:tumor /projects/acoudray/star/RNAseq/BaseRecalibration/rnaseq_added_sorted_dedup_split_recal.bam \
-PON MuTect2_PON_2samples.vcf \
--dbsnp /projects/acoudray/star/ref_genome/dbsnp_b147_hg38.vcf \
and I got some strange warning during the compilation :
WARN 18:01:55,963 SomaticGenotypingEngine - At Locus chrchr1:8685652, we detected that variant context had alleles that not in PRALM. VC alleles = [C, T], PRALM alleles = 
WARN 18:01:56,283 SomaticGenotypingEngine - At Locus chrchr1:8717782, we detected that variant context had alleles that not in PRALM. VC alleles = [A, G], PRALM alleles = 
WARN 18:01:56,458 SomaticGenotypingEngine - At Locus chrchr1:8733981, we detected that variant context had alleles that not in PRALM. VC alleles = [C, T], PRALM alleles = 
WARN 18:01:57,860 SomaticGenotypingEngine - At Locus chrchr1:8808360, we detected that variant context had alleles that not in PRALM. VC alleles = [A, C], PRALM alleles = 
INFO 18:02:03,694 ProgressMeter - chr1:8861373 0.0 5.5 m 545.7 w 0.3% 32.1 h 32.0 h
INFO 18:03:03,696 ProgressMeter - chr1:8865651 0.0 6.5 m 644.9 w 0.3% 37.9 h 37.8 h
and it seems that nothing is written in the output.
Any idea from where it comes from ?
Note : I just installed the nightly build for the 2 last steps (combining .vcf files and variant calling with mutect2). The normal-only mode to generate .vcf file in artifact_detection_mode wasn't done with the latest nightly build but with GATKv3.6 without any nightly build.
Thanks a lot !