SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to call variants from a whole genome alignment file baika Bioinformatics 7 08-30-2019 12:19 PM
Using SRMA output to call variants with mpileup gavin.oliver Bioinformatics 3 04-17-2014 09:20 AM
False negative variant calling in haploids. Call variants using coverage (not stats)? Genomics101 Bioinformatics 3 06-07-2012 11:29 AM
Doubts regarding samtools mpileup - Call somatic mutations from a pair of samples ? swapnil2188 RNA Sequencing 2 05-18-2012 06:54 AM
Using UnifiedGenotyper to call variants from haploid data? oiiio Bioinformatics 0 01-24-2012 08:29 PM

Reply
 
Thread Tools
Old 02-13-2014, 11:00 AM   #1
FrankiB
Member
 
Location: Sherbrooke

Join Date: Dec 2013
Posts: 23
Default How to call variants from two samples?

Hi,

I'm analyzing two exome deep sequencing libraries, one from cancer cells and the other from normal cells.
I have been through the GATK best practices to end with a recalibrated filtered vcf file (my last step was the Variant Recalibration).

How can I identify genetic variations found between the cancer and normal cells? I'm not interested in variations seen in my samples when
they are compared to the human genome but the differences between my normal and cancer cells.


Any help will be welcome
FrankiB is offline   Reply With Quote
Old 02-13-2014, 11:42 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,972
Default

http://www.biostars.org/p/59591/
GenoMax is offline   Reply With Quote
Old 02-13-2014, 12:14 PM   #3
FrankiB
Member
 
Location: Sherbrooke

Join Date: Dec 2013
Posts: 23
Default

Thank you very much
FrankiB is offline   Reply With Quote
Reply

Tags
variant calling, variants

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 02:40 AM.


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