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Old 10-17-2014, 03:12 AM   #8
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

@WhatsOEver: -T is useful when a file is completely missing a header. Otherwise, it doesn't do much.

@JadeB: The "[sam_read1] reference 'SN:GC01-(1934) LN:17090" means that samtools is seeing part of your header as a read. This is pretty unusual, but you're correct that this will only happen if it's not parsing the header correctly (internally, sam_hdr_read() moves the file pointer to just past the header). We're up to samtools 1.1 now, so go ahead and upgrade in any case, though I suspect there's something wrong with the header (maybe spaces rather than tabs) that will also prevent the newer versions from working. If 1.1 also doesn't work, post the first 100 or so lines (just "head -n 100 file.sam > file.txt") or so as a text file and I can have a look.
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