Hi Nenad,
You could try novosort it might do what you want. It's name sort does
primary alignment pair first and for secondary alignments uses HI tag. It
doesn't know about supplementary alignments that bwa mem produces. Can
download as part of Novoalign package at www. novocraft.com. IT's free to
use in single thread mode.
Kind Regards, Colin
On 22 October 2014 15:20, Nenad Bartonicek <n.bartoni...@garvan.org.au>
wrote:
> Dear all,
>
> Samtools (both 0.1.19 and 1.0.0) make a sorting error when sorting by
> name. (Minimal example dataset is here:
> https://pwbc.garvan.org.au/~nenbar/samtools/test.bam)
> If we look at 2 paired end reads mapping to two transcripts, the paired
> mates follow each other and their mapping to the transcripts.
>
> samtools view test.bam
>
> >HISEQ:51:C315AACXX:4:1101:1189:97694 419 *TCONS_00000145* 14 3 99M = 117
> 136
> CCATAAGCGGAGAAAGAGGGAATGACATTGTTCTTACACGGCACAAGCAGACAAAATCAACATGGTCATTTAGAAATCGGAGGTGTGGATGCTCTCTAT
> CCCFFFFFHHGHHIIJGIJJIIJJJJIJJJIJJJJIJJIJGIIJJJJJIIIJGHHGHFFFEFEEECCEDEEFDDDDDDDCBDD2?>@BCDDDDDDAAA@
> NH:i:2 HI:i:1
> >HISEQ:51:C315AACXX:4:1101:1189:97694 339 *TCONS_00000145* 117 3 33M = 14
> -136 CGGAGAAATATGGTACACCTCTTTACGTATATG ?HCA4HHEC?HHFEC?<G@ABHFDA?D?B???@
> NH:i:2 HI:i:1
> >HISEQ:51:C315AACXX:4:1101:1189:97694 355 *TCONS_00000146* 890 3 33M = 927
> 136 CATATACGTAAAGAGGTGTACCATATTTCTCCG @???B?D?ADFHBA@G<?CEFHH?CEHH4ACH?
> NH:i:2 HI:i:2
> >HISEQ:51:C315AACXX:4:1101:1189:97694 403 *TCONS_00000146* 927 3 99M = 890
> -136
> ATAGAGAGCATCCACACCTCCGATTTCTAAATGACCATGTTGATTTTGTCTGCTTGTGCCGTGTAAGAACAATGTCATTCCCTCTTTCTCCGCTTATGG
> @AAADDDDDDCB@
> >?2DDBCDDDDDDDFEEDECCEEEFEFFFHGHHGJIIIJJJJJIIGJIJJIJJJJIJJJIJJJJIIJJIGJIIHHGHHFFFFFCCC
> NH:i:2 HI:i:2
>
> However, when we sort by name, the transcripts are scrambled.
>
> samtools sort -n test.bam test.sorted
> samtools view test.sorted.bam
>
> >HISEQ:51:C315AACXX:4:1101:1189:97694 339 *TCONS_00000145* 117 3 33M = 14
> -136 CGGAGAAATATGGTACACCTCTTTACGTATATG ?HCA4HHEC?HHFEC?<G@ABHFDA?D?B???@
> NH:i:2 HI:i:1
> >HISEQ:51:C315AACXX:4:1101:1189:97694 355 *TCONS_00000146* 890 3 33M = 927
> 136 CATATACGTAAAGAGGTGTACCATATTTCTCCG @???B?D?ADFHBA@G<?CEFHH?CEHH4ACH?
> NH:i:2 HI:i:2
> >HISEQ:51:C315AACXX:4:1101:1189:97694 419 *TCONS_00000145* 14 3 99M = 117
> 136
> CCATAAGCGGAGAAAGAGGGAATGACATTGTTCTTACACGGCACAAGCAGACAAAATCAACATGGTCATTTAGAAATCGGAGGTGTGGATGCTCTCTAT
> CCCFFFFFHHGHHIIJGIJJIIJJJJIJJJIJJJJIJJIJGIIJJJJJIIIJGHHGHFFFEFEEECCEDEEFDDDDDDDCBDD2?>@BCDDDDDDAAA@
> NH:i:2 HI:i:1
> >HISEQ:51:C315AACXX:4:1101:1189:97694 403 *TCONS_00000146* 927 3 99M = 890
> -136
> ATAGAGAGCATCCACACCTCCGATTTCTAAATGACCATGTTGATTTTGTCTGCTTGTGCCGTGTAAGAACAATGTCATTCCCTCTTTCTCCGCTTATGG
> @AAADDDDDDCB@
> >?2DDBCDDDDDDDFEEDECCEEEFEFFFHGHHGJIIIJJJJJIIGJIJJIJJJJIJJJIJJJJIIJJIGJIIHHGHHFFFFFCCC
> NH:i:2 HI:i:2
>
> This causes an error in some tools (such as RSEM) that require paired
> read mates to follow each other.
>
> Is this a bug or a feature, and if a feature, how can one go around it
> without using bash sort.
>
> Cheers,
>
> Nenad
>
> Nenad Bartonicek, PhD
> Bioinformatic Officer
> Centre for Clinical Genomics
> Garvan Institute of Medical Research
> 384 Victoria Street
> Sydney NSW 2010
> Australia
>
> E: n.bartoni...@garvan.org.au
> T: +61(02)92955764
>
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