somaticseq

somaticseq copied to clipboard

SEQC2: Some high confidence SNVs and INDELs in VCF are outside of regions defined by High-Confidence_Regions_v1.2.bed

1

I downloaded high-confidence_sINDEL_in_HC_regions_v1.2.vcf.gz and high-confidence_sINDEL_in_HC_regions_v1.2.vcf.gz from FTP but noticed that some of the variants are not in the regions defined by High-Confidence_Regions_v1.2.bed. This led to issues when I compared my...

luederm

Docker issue with latest version

1

I am trying to use "BamSurgeon" which uses SomaticSeq, however there is an error that reaches that step: docker run --rm -v /home/data:/home/data -u ####:#### lethalfang/somaticseq:latest \ java ... "Error...

emucaki

AI consensus calling error on WGS samples

9

I'm trying to run somaticseq_parallel on some samples VCFs to call the AI consensus. The version for SomaticSeq is SomaticSeq v3.7.3. Version of XGBOOST is 2.0.2 I've run all mutation...

GACGAMA

Are multi-nucleotide and complex variants ignored?

2

Hi, We use somaticseq to just merge variants from Mutect2 and HMF Tools SAGE (the latter as "arbitrary" vcf's), the classification module is not used currently. However we were missing...

rebber

Output allele of the normal sample

2

Hi @litaifang, Thanks for your great tool which helps me a lot. I wonder if there is an option/parameter to output the vcf file which contains not only the allele...

fredsamhaak

Slow RNA variant calling

8

Hello, I am trying to run SomaticSeq on RNA data (single-end reads) but it's really slow. It never finished because I had to kill it after 7 days. I have...

katjur01

snakemake implementation support tumour-only samples.

1

Hi, is it possible that the snakemake implementation supports single "tumour-only" samples? It looks as though it doesn't, or at least this usage is not described. I am making a...

harrymatthews50

some indels had frequency of zero.

2

when I run somaticseq "--run-mutect2 --run-vardict --run-lofreq --run-scalpel --run-strelka2 --run-somaticseq --run-workflow ", I found some indels had frequency of zero. For example, chr1 156842000 . A AAGAAAACTGATGTAAAGTAG 0.0 REJECT MDLPK=1,0,0,0,0;NUM_TOOLS=1;LC=11.5;AF=0...

zenghp365

High-Level Diagrams of SomaticSeq's codebase

1

This PR adds onboarding documents with Mermaid diagrams that provide a high-level overview of the SomaticSeq codebase. You can see an example of how these diagrams render in another project...

ivanmilevtues

Cannot access local variable 'ith_base'

4

Hi, I generated training classifiers using the SEQ2 data and am trying to classify my data with the trained classifiers. I am working with multiple tumor-normal pairs, and some have...

pagnasok