how is the output of bcftools stats calculated?
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5.9 years ago

I have been using bcftools stats, but I’m uncertain about what several fields in the output mean. The documentation is good for what the command line options do, but has no breakdown of what the output means or how it is calculated.

This is  part of the output from vcftools stats on my file:

# SN, Summary numbers:

# SN    [2]id   [3]key  [4]value

SN      0       number of samples:      4301

SN      0       number of records:      803

SN      0       number of SNPs: 714

SN      0       number of MNPs: 0

SN      0       number of indels:       94

SN      0       number of others:       7

SN      0       number of multiallelic sites:   33

SN      0       number of multiallelic SNP sites:       2

Things I can't find in the documentation:

  • Does “multiallelic” denote “more than 2 alleles” rather than “not monomorphic”?
  • The number of SNPS+indels+others does not sum to the total number of records. Is this because an SNP can also be an indel or “other?”
  • What types of variants are covered by “others” here?
  • Why is the id[2] field blank for all sections of my output?

Thanks,

James

bcftools • 4.7k views
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To anyone looking for the answer to these questions, its here:

https://github.com/samtools/bcftools/issues/316

The poster actually posted the same question on the tool's GitHub page where the contributers responded.

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