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FOI-Bioinformatics / CanSNPer2

CanSNPer2: A toolkit for SNP-typing bacterial genomes.
GNU General Public License v3.0
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When a genome fail alignment to one ref, false result in tree pdf #13

Closed CarolineOhrman closed 4 years ago

CarolineOhrman commented 4 years ago

When a genome fail to align to a reference, these snps are still marked as ancestral "lilac" in the tree. They should be marked as missing "grey".

One example: 16-500 fail alignment to FSC200. No FSC200 snps the files but these snps are still marked as ancestral in the tree.

16-500_GCF009818075.1_2020-04-21.txt 16-500_GCF009818075.1_called_snps_2020-04-21.txt 16-500_GCF009818075.1_tree.pdf

davve2 commented 4 years ago

Should be solved by other means, will be reopened if problem occurs again