qindan2008

If I need to filter raw strelka2 somatic vcfs by SNVSB (Somatic SNV site strand bias), how the threshold should be set? Do you have any suggestions? Thank you.

How to deal with some controversial somatic and germline variants

2

For normal-tumor sample pair, when I run with somatic mode, I got a somatic variant in which normal variant allele frequency was 0.0526. 1 241680511 . T TA . PASS...

How to distinguish LOH and germline variants

1

I run strelka2 version 2.9.10 with paired normal-tumor somatic mode, and got an site which indicated that it should be LOH type. 1 241663871 . G A . LowEVS SOMATIC;QSS=30;TQSS=2;**NT=het;QSS_NT=30**;TQSS_NT=2;SGT=AG->GG;DP=296;MQ=59.12;MQ0=0;ReadPosRankSum=-1.18;SNVSB=0.00;SomaticEVS=0.00;EVSF=0,1,0.5,59.117,0,0,-1.1758,-1.3024,0,0.017964,24,63,0,0...

Difference between TumorSampleAltAlleleFraction and Somatic allele freqeuncy

2

Hello, When I run strelka2 somatic variants calling with "--reportEVSFeatures", I got variants vcfs containing values of "TumorSampleAltAlleleFraction". Those values are very close to "Somatic allele freqeuncy" in most cases....

Show segment be filtered by region width?

1

Hi, I run GATK CNV and then TitanCNA, according to the method [https://github.com/gavinha/TitanCNA/issues/38](url). The result segment file "sampleID_cluster04.segs.txt" contains many region with width equals 1. So, should segment be filtered...

How to save stand-alone html from R D3TableFilter

1

Hi, How to save D3TableFilter output to stand-alone html table with R not in shiny envirement ? Thank you very much ! Qin

generateEvents empty output

3

Hi, When I run SUPPA2 generateEvents subcommand with Bombyx_mori gtf download from EnsemblMetazoa, all output files were empty. The command I used was: **python3.4 /DataProcess/software/SUPPA-master/suppa.py generateEvents -i \ Bombyx_mori.ASM15162v1.48.gtf -o...

Error in Generating consensus clonal evolution trees across samples

1

Hello, When I run infer.clonal.models, an error occurred. y = infer.clonal.models(variants = data, cluster.col.name = 'cluster', vaf.col.names = vaf.col.names, ccf.col.names = ccf.col.names, sample.groups = sample.groups, cancer.initiation.model='monoclonal', subclonal.test = 'bootstrap', subclonal.test.model...

Hello, I have 10 pairs of samples. They're paired primary and metastasis tumors, but none of them have normal controls. Can variants called by mutect2 or other snp callers be...

install error: version GLIBCXX_3.4.21 not defined in file libstdc++.so.6 with link time reference

1

Hi, When I install gdsfmt, an error occurred as below: **installing to /home/LL/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-gdsfmt/00new/gdsfmt/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help...