[svtoolkit-help] Genome STRiP - mismatched read pair insert size error

[Anne-Katrin E. <ak...@ny...>]

Hello!

I am running GenomeSTRiP on 50 genomes (bwa-aligned, GATK indel realigned and quality recalibrated) and I am getting the following error:

##### ERROR MESSAGE: Mismatched read pair insert sizes for sample 6837: [ {HS2000-910_287:1:1309:11124:98404    97      17      22252630        0       100M    =       22251548        -983    CTTTGAAGATTTCGTTGGAAACGGGATAATCTTCACAGAAAAGCTAAACAGAAGCATTCTCAGAAACTTCTTTGTGATGTTTGCTTTCAACTCACAGAGT >@??>>?=>=??=6=?==???<6==>>>?>=??=>;><=>??==?>??<>=>9==>=?=><=>>>?;>><>@?>=?>=<>>?><=?><=5;?=><>>>>=    X0:i:5  X1:i:0  XA:Z:17,+22255009,100M,0;17,+22259766,100M,0;17,+22247875,100M,0;17,+22245496,100M,0;   BD:Z:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN    MD:Z:100        RG:Z:6837       XG:i:0  BI:Z:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN       AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  MQ:i:47      XT:A:R}, {HS2000-910_287:1:1309:11124:98404     145     17      22251548        47      2M1D98M =       22252630        981     TTTGAGAGAGAAGCTTTGAAACACTCTTTTTCTAGAATCTGCAAGTGGACATTGGGAGGGCTGTGAGGTTTGTGGTGGAAAAGGAAATATCTCCACATAA    @@>=?=?=?=>?<>=>?>?==>;=><>>>>><=><?=><=<=?>;======>>==<>====>;>=?=;??>;>=;===????==??=>=>=>>=<===@7 X0:i:1  X1:i:0  OC:Z:100M       BD:Z:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN       RG:Z:6837       XG:i:0  BI:Z:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN    AM:i:0  NM:i:4  SM:i:37 XM:i:4  XO:i:0  OP:i:22251549   XT:A:U} ]
##### ERROR ------------------------------------------------------------------------------------------

So the insert size of the left and right mate don't agree. We think that indel realignment might cause the mismatch in insert sizes. Has this error message been reported before on bwa-aligned reads (+ GATK realignment, recalibration)? Is there a way to prevent GenomeSTRiP from crashing at those instances, e.g. printing a warning instead of an error?  It only happens very rarely - on 50 high-coverage whole genomes the error was reported 4 times.

Thanks,

Anne-Katrin


--------------------------------------
 Anne-Katrin Emde, Ph.D.
 Bioinformatics Scientist
 New York Genome Center
 ak...@ny...<mailto:ak...@ny...>
 (917)-951-0167
--------------------------------------