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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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No VCF file produced #9

Closed mgalardini closed 9 years ago

mgalardini commented 9 years ago

Hi,

thanks a lot for this really interesting and useful software. In the "Quick start" page of the documentation (http://harvest.readthedocs.org/en/latest/content/parsnp/quickstart.html) the presence of a VCF file is reported i the output directory, but when running the following command I haven't got such thing.

./parsnp -g NC_000913.gbk -r genomes/NC_000913.fasta -d genomes -p 10 -v -c

This is the content of the output directory:

all_mumi.ini         parsnpAligner.ini  parsnp.ggr   parsnp.xmfa
NC_000913.fasta.ref  parsnpAligner.log  parsnp.tree  psnn.ini

I'm interested in getting the SNPs of the input genomes as compared to the reference; if that information is stored elsewhere I would be happy anyway :)

Thanks a lot, Marco

mgalardini commented 9 years ago

Sorry, just found out about harvesttools to do all the conversions. Maybe would be good to add this bit of information in the parsnp docs?

Best, Marco

treangen commented 9 years ago

Thanks Marco, this is a good suggestion, I will add additional details to the docs.