Go Back   SEQanswers > Literature Watch

Similar Threads
Thread Thread Starter Forum Replies Last Post
Structural variation detection from Exome-seq single-end data mandar.bobade60 General 0 09-21-2015 02:35 AM
variation analysis in NGS data CCBIO Bioinformatics 4 11-15-2013 02:22 AM

Thread Tools
Old 10-04-2016, 08:08 AM   #1
Lennart Johansson
Junior Member
Location: Groningen

Join Date: Aug 2013
Posts: 1
Default CoNVaDING: Single Exon Variation Detection in Targeted NGS Data

CoNVaDING (Copy Number Variation Detection In Next-generation sequencing Gene panels) is designed for small (single-exon) copy number variation (CNV) detection in high coverage next-generation sequencing (NGS) data, such as obtained by analysis of smaller targeted gene panels.

CoNVaDING makes use of a group of (at least 30) possible control samples from which the samples with the most similar overall pattern are selected as control samples. These samples are then used for read-depth normalization on all (autosomal) targets and on all targets per gene. CNV prediction is based on a combination of ratio scores and Z-scores of the sample of interest compared to the selected control samples.

Quality (QC) metrics are calculated per sample and per analyzed target.
Output is generated on three levels:

longlist: This list contains all calls, disregarding the target quality.
shortlist: This list contains a subset of the longlist, filtered on within sample target QC metrics.
final list: This list contains a subset of the shortlist, filtered on target QC metrics obtained from other samples.

CoNVaDING has been written for use of CNV detection in high coverage NGS data (at least ~200x). With lower coverages it might still work, but more targets will fail QC metrics.

The program is written in perl and has dependencies on specific perl libraries as well as on samtools.


Source code:


Lennart Johansson is offline   Reply With Quote

cnv, gene panel

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 10:07 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO