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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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VCF file does not contain indel information #137

Open Archaea810 opened 6 months ago

Archaea810 commented 6 months ago

Hello. I am currently analyzing the SNVs for 400+ fungal genomes for pangenomic analysis. I was just wondering if the indel information for the multiple sequence alignment is stored in the outputted .xmfa or .vcf format, since I can't find any. Thank you in advance.

bkille commented 6 months ago

Hi @Archaea810!

Parsnp alignments are allowed to contain indels, and in the VCF file the record will have the INDEL filter set. That being said, it is possible that Parsnp is not identifying any indels in the core-alignment for your dataset. Parsnp is a conservative alignment method and aims to exclude large indels from the core-genome.

If you look at the parsnpAligner.log file in your output directory, you should be able to see how much of the genome was captured in the parsnp.xmfa output.