Hi Nils,
After some further look, I think this might not be the fault of Picard
MarkDuplicates, but the incorrect labeling of read pairs in this BAM file. The
actual situation is that the two reads of this read pair differ by a
one-base-shift and both are chimeric reads, but in this BAM, the primary and
the supplementary alignment of each read are mis-labeled as a read pair (the
7th and 8th column). I had a samtools fixmate (version 0.1.19) step before
Picard Markduplicates, which might be the real culprit, as the error from
MarkDuplicates disappeared after I removed the fixmate step.
Cheers,
Ni
On Sep 17, 2014, at 1:26 PM, Nils Homer <nho...@broadinstitute.org> wrote:
> Hi Ni,
>
> my apologies that I have not been able to look at this. I am tracking this
> as an issue on our Picard github issues site:
> https://github.com/broadinstitute/picard/issues/72
>
> N
>
> On Fri, Sep 5, 2014 at 2:32 PM, Nils Homer <nho...@broadinstitute.org> wrote:
> Thanks Ni for the report, we will take a look at it over the next week.
>
> Nils
>
>
> On Fri, Sep 5, 2014 at 1:19 PM, Ni Huang <nihu...@genetics.wustl.edu> wrote:
> Hi,
>
> I am having the "Value was put into PairInfoMap more than once" error from
> MarkDuplicates, and it seems it's caused by chimeric reads/supplementary
> alignment produced by bwa mem:
>
> Error message:
> Exception in thread "main" htsjdk.samtools.SAMException: Value was put into
> PairInfoMap more than once. 3: 1:HW-ST997:617:HADL0ADXX:1:1114:15556:79712
>
> Reads causing problem:
> HW-ST997:617:HADL0ADXX:1:1114:15556:79712 161 chr10 124174955
> 0 45S56M chr13 91710177 0
> TATCTATATAAAAATACATACACAGACAGACAGACAGAAAGAGAGACAGACAGACAGACAGACAGACAGACAGACGGACGGACGGACGGACGGACGGACGG
>
> CCCFFFFFHHHHHJIJJJJJJJJJJJJJJJJJIIJJIIJJIIJIJJJJIIJJJJJIIJJIJJIIIIJHHFFHFFFDDDDBBDDDDBDDDDDDDDDDDDDDB
> NM:i:1 AS:i:51 XS:i:51 SA:Z:chr13,91710177,-,43S31M27S,0,0; MQ:i:0
> RG:Z:1
> HW-ST997:617:HADL0ADXX:1:1114:15556:79712 81 chr10 124174955
> 0 38S63M chr13 91710177 0
> ATAAAAATACATACACAGACAGACAGACAGAAAGAGAGACAGACAGACAGACAGACAGACAGACAGACGGACGGACGGACGGACGGACGGACGGACGGACG
>
> CDDEEDDDDDEEDDDDDDDDDDDDDDEDDDCDCDDECCEDEEFFFFFFFHHHHHHFJJIGIIJJJJJIGIGJJJIIJIFEGEHGJJJJGHHHHDDFFFCCC
> NM:i:3 AS:i:52 XS:i:51 SA:Z:chr13,91710177,+,50S31M20S,0,0; MQ:i:0
> RG:Z:1
> HW-ST997:617:HADL0ADXX:1:1114:15556:79712 2145 chr13 91710177
> 0 50H31M20H chr10 124174955 0
> TCTGTCTGTCTGTCTCTCTTTCTGTCTGTCT HHFFFFFFFEEDECCEDDCDCDDDEDDDDDD NM:i:0
> AS:i:31 XS:i:29 SA:Z:chr10,124174955,-,38S63M,0,3; MQ:i:0 RG:Z:1
> HW-ST997:617:HADL0ADXX:1:1114:15556:79712 2193 chr13 91710177
> 0 43H31M27H chr10 124174955 0
> TCTGTCTGTCTGTCTCTCTTTCTGTCTGTCT JIIJJJJJIIJJJJIJIIJJIIJJIIJJJJJ NM:i:0
> AS:i:31 XS:i:29 SA:Z:chr10,124174955,+,45S56M,0,1; MQ:i:0 RG:Z:1
>
> The version of picard I am using is version 1.119. I think picard started
> supporting the 0x800 flag/supplementary alignment since version 1.96, but
> perhaps not all modules handle those reads correctly?
>
> Is there a work-around of this issue at the moment?
>
> Many thanks,
> Ni
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds. Stuff that matters.
> http://tv.slashdot.org/
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
>
>
------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
