parsnp.vcf versus parsnp.snps

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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parsnp.vcf versus parsnp.snps #25

Closed gotero closed 8 months ago

gotero commented 7 years ago

According to the docs, parsnp.vcf is used to infer the phylogenetic tree. If so, then why does it contain the snps I want to filter out near recombination sites (-x option)? If REC and LCB snps are present in parsnp.vcf, how is parsnp.snps created?

bkille commented 8 months ago

Hi,

The parsnp.snps.mblocks file is creating with harvest-tools, and filters out any non PASS records in the VCF.