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Hi,

I run into an error at step of IndelRealigner for GATK v2.0 complaining about SAM/BAM file has inconsistent mapping information

here is the command I used (take out full path for clarity):

java -Xmx4g -jar /Path/GenomeAnalysisTK-2.1-8-g5efb575/bin/GenomeAnalysisTK.jar -T IndelRealigner -I /Path/myBam.bam -R /path/hg19.fa -targetIntervals /path/myBam.output.intervals -o /Path/my_realignedBam.bam -known /Path/bundle-1.5/hg19/Mills_and_1000G_ gold_standard.indels.hg19.sites.vcf -known /Path/bundle-1.5/hg19/1000G_phase1.indels.hg19.vcf

Here is the error message I encountered: ...

ERROR MESSAGE: SAM/BAM file SAMFileReader{/Path/myBam.bam} is malformed: read NCI-GA1:30:70BETAAXX:2:114

:10000:10163 145 chr1 * 37 108M chr14 59648529 * GCAAGACCAACAAGAAGATCGCCATTGCTAACTGTGGACAACTCTAATAAATTTGGCTTGTGTTTTATCTTAGCCACCACACTGTTCTTTCTG TAGCTCAAGAGAGTA @?BEC@BCB@DB@;=8BAB<8BDDDEFIIHEIHI>I<IIDHHIHDIIII@GIDIIIIICIIHIHIHIIIIIIBIIHIIDIHIIIIIIFIDI has inconsistent mapping information.

ERROR ------------------------------------------------------------------------------------------

...

Anybody encountered similar issue? Advice would be greatly appreciated!

Mike

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