VCF file does not contain indel information

[Archaea810]

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]

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.