SEQanswers

Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation



Similar Threads
Thread Thread Starter Forum Replies Last Post
target enrichment for resequencing using Ion Torrent JWJH Ion Torrent 0 04-22-2012 04:38 PM
PubMed: High-throughput resequencing of target-captured cDNAs in cancer cells. Newsbot! Literature Watch 0 09-21-2011 11:30 PM
Duplicates percentage in target resequencing Seq84 Illumina/Solexa 5 04-29-2011 06:16 AM
Targeted Resequencing - Target file issues LFM Bioinformatics 0 04-12-2011 04:59 AM
exon enrichment by PCR for resequencing vasvale Genomic Resequencing 2 11-07-2008 01:17 PM

Reply
 
Thread Tools
Old 10-05-2012, 04:04 AM   #1
ugm6hr
Junior Member
 
Location: UK

Join Date: Feb 2011
Posts: 4
Default PCR-based target resequencing with Illumina

I have enriched exonic regions of candidate genes with Fluidigm Access Array (microfluidic PCR-based) to create libraries from human DNA. The resequencing is on Illumina HiSeq.

Does anyone have experience of variant calling issues with PCR-based enrichment on Illumina sequencing data? We cannot remove / mark duplicates as we would normally with GATK, due to the target enrichment process. I'm unclear what effect this has on variant call quality metrics.

Thanks.
ugm6hr is offline   Reply With Quote
Reply

Tags
fluidigm, gatk

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 12:17 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO