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
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