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.
John
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