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Old 04-11-2011, 05:45 AM   #1
pallo
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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?
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