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Did anyone solved the incompatibility of .bam files by TMAP with GATK?

Hi All,

I am having problem with .bam from Ion Torrent too: I sorted, reordered, marked duplicates, also added the RG in picard like this: RGID=019 RGLB=019 RGPL=IONTORRENT RGSM=019 RGPU=none. 019 is my sample id.

GATK didn't complain when generating realigner.intervals. But got error message when running GATK IndelRealigner:
MESSAGE: SAM/BAM file SAMFileReader{019reordered.bam} is malformed: the BAM file has a read with no stored bases (i.e. it uses '*') which is not supported in the GATK; see the --filter_bases_not_stored argument. Offender: 7T3ID:1010:2116

Has anyone solved the problem yet? What is the correct way to do that? Thanks a lot!

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