Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa

Similar Threads
Thread Thread Starter Forum Replies Last Post
Finding CNVs in tumors, no control, WES - Which programs should I use? Miau Bioinformatics 0 08-01-2014 03:06 AM
NGS whole genome sequence versus sequence capture for quality control houkto Bioinformatics 0 02-02-2012 05:16 AM
PubMed: Control-free calling of copy number alterations in deep-sequencing data using Newsbot! Literature Watch 0 04-08-2011 02:10 AM
Sequence Alignment Quality Control nilshomer Bioinformatics 4 02-06-2010 08:24 AM

Thread Tools
Old 02-12-2015, 09:28 AM   #1
Junior Member
Location: South Central US

Join Date: Aug 2012
Posts: 7
Default WES - how deep do you sequence your germline control

Hello Seqers,

we currently do WES with a mean coverage of ~120x for tumor as well as the germline samples. Since we only use the germline to help us with the somatic alteration calls I was thinking about cutting the coverage of the germline samples in half to free up some real estate on the flowcell. Does any one have experience with this?

Thanks, O.
onconaut is offline   Reply With Quote
Old 02-12-2015, 12:45 PM   #2
Senior Member
Location: UK

Join Date: Jan 2010
Posts: 390

We'd normally do 50x on the normal and 100x+ on the tumour - I think that's quite a common strategy.
Bukowski is offline   Reply With Quote
Old 02-12-2015, 01:55 PM   #3
Location: USA

Join Date: Aug 2013
Posts: 52

It depends on your downstream processes. If you are simply calling SNVs then it doesn't really matter. But for other applications (eg. CNVs), many programs prefer to have similar coverage between your tumor and normal. Even if they don't require it, you are getting rid of other sources of variation (eg. by capturing the same amount of DNA in the same exome hyb reaction).
bilyl is offline   Reply With Quote

coverage depth, germline, illumina, wes

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 01:34 AM.

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