sahuno
cancer genomics @Polak lab; cell-free DNA, mutational signatures, cell of origin
- Total activity 41
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 4
- Subscriptions 13
Posts
Recent activity by sahuno Sort by recent activity-
Somatic Hotspot mutation is filtered although evident with IGV
AnsweredHi allI can't find evidence of key mutations after Mutect2 (Tumor-Normal Mode with PoN). On the other hand, I do see the mutation with IGV and i don't know why it was filtered. For example, patie...
-
No t_depth in Funcotator MAF
AnsweredIs there a way to enable t_depth in Funcotator MAF ? however my final maf contains some info on depth "tumor_f","t_alt_count","t_ref_count","n_alt_count","n_ref_count" Thanks in advance -S GAT...
-
For mislabelled Tumor & Normal bam files from same patient, which gatk tool approach can i use to reclassify?
Please if I have mislabelled bam files (1 should be tumor & the other germline bam file) from same patient which approach or gatk tool can i use to correctly reclassify tumor & germline bam files? ...
-
[Funcotator] java.lang.IllegalArgumentException: Unexpected value: lncRNA
Can you please provide a) GATK version used; "broadinstitute/gatk:latest" (gatk 4.1.8.1) Hello I'm running funcotator on germline samples but keeps throwing this error ` java.lang.IllegalArgumentEx...
-
How can i remove chr_Un* from somatic cnv plots?
Can you please provide a) GATK version used - gatk 4.1.6.0.(snapshot and seg file attached) Hello how can i remove the chr_Un* regions in my copy number plots?My model final segment file doesn't ...
-
munmap_chunk(): invalid pointer [FilterAlignmentArtifacts task in mutetct2 workflow]
Hello GATK Team, I'm running somatic variant calling (mutect2) on 108 Whole Exome Tumor-Normal samples in Terra. However, one of the samples keeps failing at `munmap_chunk(): invalid pointer` at F...
-
WARN MinimalGenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location chr11:294512
Dear GATK, Question; any suggestions on how to resolve this? i run `GenoytypeGVCFs ( gatk/4.1.6.0)` on a cohort of cancer patients but run into this warning message. `08:19:05.902 WARN MinimalGeno...
-
Error using a edited gatk wdl (bam-unmapped-bam workflow) to accept array[files] as input rather than a single .bam file
Dear GATK, I modified a `gatk pre-processing wdl workflow` (`bam-unmapped-bam`) to accept an array of files rather than a single `.bam` file as input but keeps throwing an error when i run. `Failed...
-
How to transform interval list with 297,694 lines to <30,000 lines to run Haplotype-caller in Terra?
Dear GATK! my aim is to transform an interval file (Exome-Agilent_V6_UTR.bed with 296,037 lines) to have <30,000 lines to be able to run GATK-haplotype-calller with germline samples on Terra (forme...