Thanks for your help with this.
Related to this topic, I am having difficulty with the SAM-to-BAM tool not showing any genome as an option for a built-in genome, despite the fact that the T2T genome is set as the reference genome for the file I am trying to convert. Is the T2T genome not recognized by this tool specifically?
Hi @TTP
Matching up the database is usually important but this tool is a little bit special. No genomes are indexed, not just the the human T2T.
But good news – your SAM file is already coordinate sorted, so you can use the “without sorting” version instead. Now, I haven’t specifically tried this with the T2T genome at all or any others recently, so if you get an error please do report that.
If for some reason you’d like a different sort order – apply that once already in BAM format. The datatype will change based on the content (qname_sorted.bam, unsorted.bam). Most tools expect the default datatype bam and those are always coordinate sorted in Galaxy. Upload + most tools apply that as a final step when creating the .bai index.
Hope that helps!
Thanks. I tried using it with the “without sorting” option but this fails to run. It did work with a genome build fasta uploaded to the history though, so this is what I am using currently. Just wondered if I was missing something here but I guess not…
2026 Update: Is your genome not indexed? No problem! Load up the fasta for your assembly and use it as a custom-genome
FAQ: How to use Custom Reference Genomes?
Thanks for letting us know and yes, using the fasta from UCSC is the alternative. 
