Vcfstats doesn't show the MNPs?

pwwang / vcfstats

Powerful statistics for VCF files

https://pwwang.github.io/vcfstats/

MIT License

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Vcfstats doesn't show the MNPs? #3

Closed LaurenceKuhl closed 2 years ago

LaurenceKuhl commented 3 years ago

Hi there,

I was trying to produce plots with vcfstats and it doesn't seem to represent MNPs (multiple nucleotide polymorphisms) as reported by bcftools stats ? I also notice a discrepancy in SNPs/Indels between bcftools and vcfstats, has this ever happened to you ? I'll take any information I can get, thanks! Best, Laurence

pwwang commented 3 years ago

Hi Laurence,

vcfstats does not have any internal variant filtering, meaning all should be included. Could you provide a minimal example vcf file and the commands of both vcfstats and bcftools you used?

Thanks, Panwen

pwwang commented 2 years ago

Closing as lacking information. Feel free to reopen.