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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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Reference Sequence SNP Call #118

Closed hdesale2408 closed 9 months ago

hdesale2408 commented 2 years ago

Hello, I ran parsnp using a 17 whole genomes. I picked one of these genomes to use as a reference, but kept the sequence file in the directory still. After running parsnp I looked at the VCF output and it seems that there are SNPs being called when the reference sequence is mapped against itself. Does this make sense? It should be the exact same sequence mapped against each other, so why would there be SNPs?

Thank you!

bkille commented 10 months ago

Hi @hdesale2408,

Sorry for the delay in responding. Yes, there should not be SNPs between the same sequence in an alignment. There have been some noted (but rare) issues w/ Parsnp incorrectly parsing .gbk files. Did your input contain .gbk/.gb files by any chance?

bkille commented 9 months ago

Hi @hdesale2408,

This bug has been fixed in Parsnp 2.0. Please let me know if you continue to experience it!