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
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:
Which behaves and gives me an index file of 7.6M.
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?
samtools index <bamfile>
java -jar BuildBamIndex.jar
samtools idxstats
Anyone seen this weird behaviour before?
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