SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Problem removing duplicate reads? (samtools and picard) cbl Bioinformatics 19 09-17-2015 11:01 AM
How to get index files using picard muzz56 Bioinformatics 9 09-30-2014 05:04 PM
Samtools's rmdup vs. Picard's MarkDuplicates fah Bioinformatics 30 10-28-2013 12:28 AM
samtools picard SamFormatConverter Bio.X2Y Bioinformatics 3 07-08-2013 07:46 AM
Samtools - index Kath Bioinformatics 2 11-24-2010 09:06 AM

Reply
 
Thread Tools
Old 04-11-2011, 05:45 AM   #1
pallo
Member
 
Location: Land of ice and snow

Join Date: Oct 2009
Posts: 10
Default samtools vs picard index

I just stumbled upon something weird. I have a library specific bam file, with several illumina lanes of PE data merged. The file is coordinate sorted and I wanted to index it, like I have past several years, with

Quote:
samtools index <bamfile>
The original bam file is 7G and I could not believe my eyes when the resulting *.bai file was 14G, so I repeated a few times with the same results. I then decided to test Picard:

Quote:
java -jar BuildBamIndex.jar
Which behaves and gives me an index file of 7.6M.

Quote:
samtools idxstats
Yields the same results for both (although it takes much longer with the larger index file, presumably just I/O)

Anyone seen this weird behaviour before?
pallo is offline   Reply With Quote
Old 04-11-2011, 03:59 PM   #2
lh3
Senior Member
 
Location: Boston

Join Date: Feb 2008
Posts: 693
Default

you should report to samtools-help@lists.sourceforge.net
lh3 is offline   Reply With Quote
Reply

Tags
index, picard, samtools

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 08:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO