Problem understanding the outputs of VarSim · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Problem understanding the outputs of VarSim

Hello everyone. Hope all of you are fine. I am starting a project related to somatic variant calling. We want to do a benchmarking with several variant callers. I have been looking for tools to produce like syntethic samples and the truth VCF. I found bamsurgeon and VarSim. I am trying to use VarSim in its somatic option, but I don't understand the outputs. I supposed the tool produces the truth VCF to compare, the simulated reads and the tumor BAM, but only generates tumor reads (?) and the truth VCF. How should I used those to do the benchmarking?

Thank you!

benchmarking calling varsim synthetic

• 675 views • link

updated 3.5 years ago by Istvan Albert

• written 3.5 years ago by Paula Andrea •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Somatic truth set
written 3.4 years ago by samuel

Does anyone know if there is a somatic truth set vcf available? I know there are now several available for germline samples from [GIAB][1] I …
somatic variant calling
written 5.4 years ago by nikitanaik224 •

I am looking for tools/methods for somatic variant calling for unpaired samples. The somatic variant calling through GATK best practices is specifically for tumor/normal paired …
Extracting the reads counts (coverage) a specific variant allele from a Fastq file
written 6.8 years ago by a.james

Hi All, Say, I have a paired-end `fastq` reads from 2 lanes, and `vcf` file with variant allele. These I have generated using the `varsim` …
how do you do variant calling on tumor samples without a normal tissue sample
written 8.6 years ago by b10hazard •

I read a paper on somatic variant callers for tumor tissue and I have a few questions. The variant callers seem to work by subtracting …
NGS data simulation: VarSim or BAMSurgeon?
written 9.5 years ago by user230613

Hi there, I want to generate NGS data to do some test and benchmark in both **germline** and **somatic** variant calling. I've read a lot …
Variant Calling in Somatic mode
written 9.8 years ago by Paul

Dear users, I am starting to play with open source variant callers such as - **MuTect, SomaticSniper, Strelka, Varscan2**. All those algorithms need always - …
The problem with sensitivity analysis of somatic variant caller
written 10.3 years ago by phongphak.06 •

Hello! I'm working on somatic variant identification from cancer samples. So, I try to simulate Illumina paired-end read with known variants by using VarSim (http://bioinform.github.io/varsim/), …
Are all CNAs of HCC1153 cell line reported by COSMIC somatic mutations?
written 10.4 years ago by lyz10302012

I am using HCC1153 and HCC1954 from TCGA Mutation/Variation Calling Benchmark 4 for benchmarking SCNA calling. However, I found some SCNAs reported by COSMIC are …
validation data sets to benchmark somatic variant callers
written 10.8 years ago by severine •

Hi Would appreciate guidelines on where to find recent, well-accepted and preferably publicly available validation datasets to benchmark both the sensitivity and specificity of somatic …
How To Produce Simulated 'Synthetic' Sequences
written 16.1 years ago by Stefano Berri

<p>Hi.</p> <p>I would like to find a program that produces simulated (Illumina GAII) reads starting from a fasta file of the genome and a series …