SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK BaseRecalibrator error message lre1234 Bioinformatics 10 07-09-2014 06:50 AM
GATK BaseRecalibrator ejects with no error! FGponce Bioinformatics 1 05-20-2013 09:45 AM
gatk bam is malformed carolW Bioinformatics 2 05-09-2013 12:59 AM
multiple BAM GATK unifiedgenotyper output memento Bioinformatics 0 02-22-2012 08:12 AM
casava 1.8 bam conversion to gatk bam kingsalex Bioinformatics 1 02-14-2012 11:47 AM

Reply
 
Thread Tools
Old 06-04-2013, 04:59 AM   #1
lre1234
Senior Member
 
Location: US

Join Date: Aug 2011
Posts: 105
Default GATK BaseRecalibrator -output bam

Hi,
I am doing my post-alignment processing on whole genomes (~40X) coverage. My aligned bam files are each ~100GB in size. After I go through all of the steps (indelrealigning, fixing mate-pairs, basereaclibrating, etc), my final output bam file after the BQSR print reads has dramatically jumped in size. They have gone from the ~100GB in size to over 120GB in size. Is this a normal occurrence and something to be alarmed by?
Thanks
lre1234 is offline   Reply With Quote
Reply

Tags
gatk, printreads

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 10:43 AM.


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