CollectGcBiasMetrics.jar

[doc2r]

Hi there,

When I run PICARDs CollectGcBiasMetrics.jar I get the following error message



Exception in thread "main" net.sf.samtools.SAMException: Exception counting mismatches for read XXXXXX_0164:6:6:3247:26441#0 1/2 100b aligned read.
at net.sf.samtools.util.SequenceUtil.countMismatches(SequenceUtil.java:251)
at net.sf.samtools.util.SequenceUtil.countMismatches(SequenceUtil.java:204)
at net.sf.picard.analysis.CollectGcBiasMetrics.doWork(CollectGcBiasMetrics.java:15
2)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at net.sf.picard.analysis.CollectGcBiasMetrics.main(CollectGcBiasMetrics.java:94)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 135374737
at net.sf.samtools.util.SequenceUtil.countMismatches(SequenceUtil.java:237)
... 4 more


I know the read XXXXXX_0164:6:6:3247:26441#0 1/2 maps to the telomeres and one maps off the end (this error I was able to "SILENT")but I really can't see what the problem. Any advice... Sequences are below





XXXXXX_0164:6:6:3247:26441#0 163 chr10 135374442 23 21M1I26M52S = 135374638 297

TTAGGGGTTAGGGTTGGGTTAGGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGAGGGGTGGGGGGAGGGGTGTGGGGTGGGTGTGGGTGGGGGTGGG

HHHHHFHAEAEEE?EGEE5B@DGDDCD?GGE7B5E<=4@<<@1<6C#####################################################
XC:i:48 XT:A:U NM:i:1 SM:i:23 AM:i:23 X0:i:1 X1:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:47


XXXXXX_0164:6:6:3247:26441#0 83 chr10 135374638 23 1S47M1D4M1D48M = 135374442 -297
TAGGGTTGGGGTGAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTAGGGTAGGGTTAGGGTTCGGGTTCGGGTTCGGGTTCGGGTTCGGGTTCGGGT

##@?@@*@?DC/ACEDE>DBCB7ABEEF@E6FFDBG8GGFFFFFFEF@GEFGGGGGGFFFF@GFEFEFGGGGGFGGGGGGGGGGGGGEGGGFGGGGB

XC:i:99 XT:A:M NM:i:13 SM:i:23 AM:i:23 XM:i:11 XO:i:2 XG:i:2 MD:Z:5G0A16G23^G4^T12G0A5A5A4G0A5A5A4

[rpauly]

Did you find a solution to this? I am having the same problem...
Exception in thread "main" net.sf.samtools.SAMException: Exception counting mismatches for read HWI-ST1392:125:C1HB2ACXX:5:2209:1874:47375 1/2 100b aligned read