John
You are right!
Here is a short fragment of the file where the sorting starts to be incorrect.
D00689:262:CAUR4ANXX:1:2210:12001:8808/1 99
AMEXGS_00350000072 1073537649
D00689:262:CAUR4ANXX:1:2212:4262:62218/2 131
AMEXGS_00350000072 1073537662
>>> Incorrect sorting beyond this point
D00689:262:CAUR4ANXX:1:1311:7571:42633/1 115
AMEXGS_00350000052 1073757534
D00689:262:CAUR4ANXX:1:1209:14064:92038/1 115
AMEXGS_00350000052 1073762716
D00689:262:CAUR4ANXX:1:1207:19595:38302/1 67
AMEXGS_00350000066 1073768421
D00689:262:CAUR4ANXX:1:1202:12406:98751/1 83
AMEXGS_00350000071 1073787822
D00689:262:CAUR4ANXX:1:1205:7367:92746/2 131
AMEXGS_00350000050 1073798500
The reads map beyond 1,073,741,824.
I guess I’ll just write a small sorting utility.
Thank you!
Best regards
Sergej
Dr. Sergej Nowoshilow
Post-doc in Tanaka Lab
Elly Tanaka group
Animal models of regeneration
Campus-Vienna-Biocenter 1
1030 Vienna
email: sergej.nowoshi...@imp.ac.at
phone: +43 (0) 1 79730 3203
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Von: John Marshall <john.w.marsh...@glasgow.ac.uk>
Datum: Samstag, 10. März 2018 um 09:55
An: "Nowoshilow,Sergej" <sergej.nowoshi...@imp.ac.at>
Cc: "samtools-help@lists.sourceforge.net" <samtools-help@lists.sourceforge.net>
Betreff: Re: [Samtools-help] Extremely long reference sequences
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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