I just tried using GSAlign and ran into something strange in the VCF that looks like a bug to me. For certain reference sites there are multiple variants listed that each have a difference reference base. For example:
contig_10_pilon 6241247 . A g 100 TYPE=SUBSTITUTE
contig_10_pilon 6241247 . T c 100 TYPE=SUBSTITUTE
contig_10_pilon 6241249 . A c 100 TYPE=SUBSTITUTE
contig_10_pilon 6241249 . T g 100 TYPE=SUBSTITUTE
I'd be happy to provide my original fasta files if you wish to pursue this and would find it useful to reproduce the error.
Hello,
I just tried using GSAlign and ran into something strange in the VCF that looks like a bug to me. For certain reference sites there are multiple variants listed that each have a difference reference base. For example:
contig_10_pilon 6241247 . A g 100 TYPE=SUBSTITUTE
contig_10_pilon 6241247 . T c 100 TYPE=SUBSTITUTE
contig_10_pilon 6241249 . A c 100 TYPE=SUBSTITUTE
contig_10_pilon 6241249 . T g 100 TYPE=SUBSTITUTE
I'd be happy to provide my original fasta files if you wish to pursue this and would find it useful to reproduce the error.
Thanks, Sophie