Somatic
Show all
Sort by newest post
-
mutect2 turm-only pipeline missing low AF0 votes 0 comments
-
Mutect2 missing a low AF known deletion0 votes 4 comments
-
mutect2.bam could not find the mutation, but bqsr found the mutation Answered0 votes 1 comment
-
mutect2 genotyping wrong? Answered0 votes 1 comment
-
Mutect stats table not found.0 votes 1 comment
-
How to decrease the likelihood threshold for a candidate haplotype to be called as a genotype in Mutect2 Answered0 votes 9 comments
-
GGA-mode gives PASS tag while the site failed in the normal workflow0 votes 13 comments
-
Error while running ModelSegments Answered0 votes 3 comments
-
Mutect2 Funcotator interval error Answered0 votes 3 comments
-
Called Somatic Mutations High Frequency of C>A SNVs Answered0 votes 6 comments
-
empty pon vcf file Answered1 vote 1 comment
-
Funconator's ignore-filtered-variants is not a recognized option Answered0 votes 1 comment
-
missing file: Callset.json , when creating PON Answered0 votes 3 comments
-
MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true does not add DS and DI tags in the output BAM file Answered0 votes 3 comments
-
SAMException: Value was put into PairInfoMap more than once Answered0 votes 5 comments
-
Why do I see a variant called by mutect2 in my matched-normal sample when checking the results? Answered0 votes 10 comments
-
Mutect2 calls long deletion with absolutely zero read support Answered0 votes 1 comment
-
Deletion is split into two deletions Answered0 votes 1 comment
-
Running Mutect 2 with matched normal vs tumor mode0 votes 3 comments
-
Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries? Answered0 votes 12 comments
-
Not generating denoisedLimit4.png with PlotModeledSegments0 votes 4 comments
-
Mutect2 issue with --force-active: not all regions are active Answered1 vote 25 comments
-
Incorrect Annotation from Funcotator Answered0 votes 5 comments
-
merge nearby variants in vcf from mutect2 Answered0 votes 1 comment
-
gatk stack memory insufficient to run Mutect2 for artifact correction Answered0 votes 1 comment
-
Mutect2 genotype-germline-sites filtering discrepancy Answered0 votes 4 comments
-
Error running mutect2 on SAM files remapped to hg38 (original reads were aligned to hg19). Answered0 votes 1 comment