Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Structural variation detection using BreakDancer on Whole Genome SOLiD data tez Bioinformatics 5 01-20-2012 07:46 AM
PubMed: VarSifter: Visualizing and analyzing exome-scale sequence variation data on a Newsbot! Literature Watch 0 01-03-2012 03:00 AM
CNV variation effects on exome sequencing? wrighth Bioinformatics 0 12-21-2010 12:43 PM
PubMed: Ultra High Throughput Sequencing in Human DNA Variation Detection: A Comparat Newsbot! Literature Watch 0 10-12-2010 04:50 AM
Seeking advice on setting up a breakpoint detection Baseless Bioinformatics 0 03-08-2010 12:54 PM

Thread Tools
Old 11-29-2011, 08:33 AM   #1
Junior Member
Location: Taiwan

Join Date: Oct 2010
Posts: 2
Question Variation detection in exome data - need advice

I have a pair of tumor/normal exome data (Illumina, paired-end) and would like to call somatic variations like mutation, indel, ... etc.

However, read 2 of the dataset is of poor quality and lead to ...
1. A mapping rate just half of the rate of read 1.
2. More artificial interchromosome read pairs

What bothers us a lot is the dramatic reduction of "effective coverage" (and thus insufficient) since many Variation Callers seem to selectively ignore some read pairs.

We've tried some softwares and have a guess from the result that ...
1. CASAVA considers only good read pairs
2. VarScan considers only good read pairs
3. GATK considers both good read pairs and singletons but not interchromosome read pairs.
It seems that GATK is the program that make the best use of all reads so far.

Does anyone have advice on how we could further rescue the coverage or what tools/methods(view it as single-end read?) we can try with this dataset ?
Any advice would be greatly appreciated.
shw is offline   Reply With Quote

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 01:15 PM.

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