Closed vivekbhr closed 6 years ago
Hi Vivek,
I have been thinking about this point as well, but at the time SNPsplit is run there is actually no reference to which strain is genome 1 or genome 2 anywhere in the BAM file. In fact, the genomes may even have been constructed by other means than SNPsplit_genome_preparation
, so there may not even be a such a thing as strain names. The output of SNPsplit consistency calls the reference (in the SNP file) genome 1, and the alternative base genome 2, so in a way we left it to the user to keep track of which genome they used as reference and which is the alternative.
I guess we could offer to add an option to input something like --genome1_name
and --genome2_name
when SNPsplit gets run so that this will then be used instead of simply calling it genome 1/genome 2?
True.. if genome were prepared by other means then genome 1 and 2 name would have to be externally provided.. Although then the users can themselves substitute the names after sorting as well, so I have no strong preference on this.
Hi @FelixKrueger
During
SNPsplit sort
, the strain names of the bam files are not entered (the suffix says_genome1
and_genome2
). neither is it printed in theSNPsplit sort
log files. The only way to find out what genome1 and 2 correspond to is to look back at the log ofgenome_generate
.It would be good to either replace the suffix
_genome1/2
with strain ID or (probably even easier) to print the strain name for genome1 and 2 in the log file ofSNPsplit sort
Thanks.. Best, Vivek