If the species name in the bam header (eg Mus musculus) does not match the species name in the flag.vcf.config.ini file (eg MOUSE) the flagging step fails. You can not just pass caveman.pl the correct species name, as found in the config file, because the bam header name overrides the command line parameter in the script.
If the species name in the bam header (eg Mus musculus) does not match the species name in the flag.vcf.config.ini file (eg MOUSE) the flagging step fails. You can not just pass caveman.pl the correct species name, as found in the config file, because the bam header name overrides the command line parameter in the script.