On 9 Mar 2018, at 23:56, Nowoshilow,Sergej 
<sergej.nowoshi...@imp.ac.at<mailto:sergej.nowoshi...@imp.ac.at>> wrote:
Apparently, the BAM file is not quite correctly sorted after all. A simple test
samtools view test.sorted.bam | cut -f3 | uniq
proofs that it is indeed the case, since the scaffold IDs are sorted over ~90% 
of the file (e.g. from scaffold001-scaffold100), while the last 10% are not 
sorted at all, e.g. scaffold052 may follow the scaffold100 an so on. Therefore, 
the problem is rather "samtools sort" and not "samtools index".

Does this jumbled last 10% consist of reads mapped at locations beyond 2^30? I 
suspect you have rediscovered https://github.com/samtools/samtools/issues/615 
which it appears fell off the samtools maintainers' to-do list and was never 
fixed. Alas.

Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
Samtools-help mailing list

Reply via email to