Are all CNAs of HCC1153 cell line reported by COSMIC somatic mutations? · Biostar

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

Are all CNAs of HCC1153 cell line reported by COSMIC somatic mutations?

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 germline CNVs (both tumor and normal sample has 0 copy (no reads) by viewing bams with IGV). Can anyone tell me how can I find the ground truth set of SCNAs for these two samples?

tcga benchmark 4

• 1,896 views • link

written 10.4 years ago by lyz10302012

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Best Practices for Tumor-Only WES Data Analysis: Seeking Feedback on Variant Calling Pipeline
written 1.9 years ago by George •

Hello everyone, I’m currently working on a pipeline for analyzing tumor-only WES data, which I understand has its challenges and limited resources available. I’d greatly …
Detection of biallelic mutation (inactivation)
written 5.2 years ago by CY

By biallelic mutation (inactivation), I mean several cases: 1) The first mutation is inherited (germline) mutation and the second mutation occurs as somatic **at other …
Tool: ClinCNV: CNV detection from short reads
written 6.8 years ago by German.M.Demidov

Dear community members, we've prepared a tool for CNV detection (another one) called *[ClinCNV][1]*. It was already used for the analysis of around 5 thousands …
Concept of Matched normal vs. Virtual Normal
written 8.9 years ago by sutturka

I have a question about the **matched normal sample vs virtual normal sample**. By definition, a matched normal (MN) is a sample of healthy tissue …
Where is the ground truth set of SCNAs for TCGA Mutation/Variation Calling Benchmark 4?
written 10.4 years ago by lyz10302012

Hi, Can anyone tell me how can I find the ground truth set of SCNAs for TCGA Mutation/Variation Calling Benchmark 4?
Tool: CRAVAT: a web tool to annotate and analyze cancer variants
written 10.8 years ago by Collin

[CRAVAT][1] provides high-throughput services for researchers to annotate and prioritize small-scale exome variants and genes discovered in normal tissues and cancers. Annotations include TARGET drug …
Identify Germline Mutations
written 12.5 years ago by yliuboston •

<p>Hi everyone,</p> <p>I am now trying to identify germline mutations from tumor and matched normal samples in TCGA and also I need to know this …
Variant Filtration And Surprising Results
written 12.5 years ago by ao.carson •

<p>Greetings,</p> <p>I have been working on a comparison of a human endocrine cancer, matched with normal tissue from the same organ. The tissue was dissected …
Data Set Suitable For Comparing Wgs, Exome, And Rna-Seq Data Generated From The Same Samples
written 13.5 years ago by Malachi Griffith

<p>Is anyone aware of a publication or pre-publication data set that includes the following for a single human tumor/normal sample pair:</p> <ul> <li>Illumina whole genome …
Tool: Varscan: Variant Detection In Massively Parallel Sequencing Data
written 14.3 years ago by Istvan Albert

[VarScan][1] is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, IonTorrent, Roche/454, and similar instruments. The newest version, …