Hello, I crammed a bam file using samtools view with the -T option, and the cram was produced. When I looked at the @SQ headers, I saw several chromosomes not in my reference fasta file. It turned out I used a build of the genome that was not used to produce the original bam file. It also looks like if the genome build following a -T option is wrong, samtools view will look for it elsewhere, as follows (from http://www.htslib.org/doc/samtools-1.1.html):
" The search order to obtain a reference is: Use any local file specified by the command line options (eg -T). Look for MD5 via REF_CACHE environment variable. Look for MD5 in each element of the REF_PATH environment variable. Look for a local file listed in the UR: header tag." I assume what happened is my "-T fasta" was wrong and so it looked elsewhere and found the correct file. Is there a way to get an output notifying that the -T fasta has been skipped? While it worked this time, it's important to know when this is happening. Best regards
_______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
