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Hi,
When we analyse Myeloid panel (TWIST) we noticed that Balsamic detects duplication in KMT2A gene between exons 2-8 or 2-10 in two ways:
1) as SNVs and INDELs where we see VAF
2) as SVs and we d…
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**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
Would it be possible to view th…
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`chr11 95796274 Minda_20 N . PASS SVLEN=5834;SVTYPE=DEL;SUPP_VEC=PB_ID_48786_2,PB_d_63,ONT_ID_38610_2,ONT_d_26,ILL_MantaDEL:184951:0:1:0:0:0,PB_severus_DEL1225,ONT_severus_DEL1326,PB_Sniffles2.DEL.2E…
jzook updated
1 month ago
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Hello and thank you for releasing this tool.
The code below (which I am assuming is there to filter multi-allelic sites) causes issues when using Deepvariant's VCFs. Deepvariant uses `Number=A` for…
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I run the ~last~ latest version of vcf2maf on my data. I want to obtain ~vcf~ VAF comparable to data from TCGA.
I could not find VAF in the maf file of variants from tumor and normal
`"vcf2maf.pl --…
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I am not able to fully understand the use of the Strand bias filter and RMxN(R3X6) filter in case of somatic variant calling.
For eg.: 1. how the RMXN filter works when a variant is found in the fo…
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### Installation Type
Docker
### pVACtools Version / Docker Image
Docker container, version 4.4.1
### Python Version
_No response_
### Operating System
_No response_
### Descri…
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Reason for this error is that I am on a case sensitive file system. so Elite/Vaflinks/Block/CMSList.php is not able to be included because it's looking for Elite/Vaflinks/Block/Cmslist.php
So this in…
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**TODO**
- [x] Generate table with the following columns {sample name, # variants in primary xls, # of variants in calls xls, # variants imputed, total number of variants in sample}
- [x] Generate…
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Since the update of the VAF.Extensions from 1.2 to 1.3 (VAF 2.2 to 2.3), the background tasks that were created using the TaskQueueBackgroundOperationManager can no longer run in parallel.
For me it …