Re: bamtools merge not sorting properly?
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Derek
Jun 28, 2012, 5:17:21 PM6/28/12
to bamtoo...@googlegroups.com
If the input BAMs are sorted, then the merged file should be sorted as well.
- Derek
On Thursday, June 28, 2012 4:58:03 PM UTC-4, lancep...@gmail.com wrote:
On Thursday, June 28, 2012 4:58:03 PM UTC-4, lancep...@gmail.com wrote:
Using the latest version of bamtools, when doing a merge of sorted bam files, the output is not sorted properly. Running samtools index (and other things) on the resulting output results in sorting errors. Is there a flag or something I am missing? Or is this not a supported feature of bamtools merge? I can't really find much documentation on this.
Michael Siebauer
Jul 2, 2012, 4:39:48 AM7/2/12
to bamtoo...@googlegroups.com
Can you try to use the BamTools API
indexing function instead of "samtools index".
I often observe problems when I try to load indexes with BamTools if they were created by samtools. :-/
bam_reader.SetSortOrder(BamMultiReader::SortedByPosition);
bam_reader.CreateIndexes();
I often observe problems when I try to load indexes with BamTools if they were created by samtools. :-/
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