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Old 07-16-2011, 08:13 PM   #3
Junior Member
Location: Salt Lake City

Join Date: Jun 2011
Posts: 9

Hi - I received the same error. I also reheadered my sam file and then tried to convert to a bam and received the [sam_read1] reference 'chrX' is recognized as '*'.

Did you ever figure out a solution to the problem?

I noticed that samtools did write a bam file. So, I visualized it (after sorting and indexing it) and it appears that the rest of the chromosomes did convert except for the chrX. I have no reads there. Not surprising.
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