Your BAM file appears to be based on the human genome, but it is not the version hosted as hg19 at the public Galaxy servers (how the data is currently labeled, and the genome selected with Freebayes originally).
This is what the error is reporting: mismatched chromosome identifiers
More about the different human genome assemblies is here.
This guide has more details about how those kinds of check are done at a detailed level.
Your data might be based on hg_g1k_v37. If yes, you can use Freebayes against that human genome reference. I would try this first.
- Update: this will work if you add in default Read groups to the BAM file with the tool AddOrReplaceReadGroups. This results in a VCF from Freebayes but it is not annotated. If you want to create an annotated VCF, then you’ll need to try the next suggestion below instead, starting from the fastq reads.
The other option is to extract the fastq reads out of the BAM you have, then to map against a version of the human genome we host and proceed to downstream steps that way. This is probably the cleanest way to create the file you want (a VCF file) or to obtain rs identifiers, but this might mean that the data can’t be used in other external applications (because they are expecting data based on a different human genome assembly!).
- bedtools Convert from BAM to FastQ
If the goal is to just learn if the data includes any known SNP rs identifiers, you can do that, and following this protocol with a single sample, from the starting reads, is what to try.
Hope that gives you some options!