SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   samtools vs picard index (http://seqanswers.com/forums/showthread.php?t=10670)

pallo 04-11-2011 05:45 AM

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?

lh3 04-11-2011 03:59 PM

you should report to samtools-help@lists.sourceforge.net


All times are GMT -8. The time now is 07:20 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.