Plugin mendelian

This plugin is intended for detecting Mendelian inconsistencies. On input the program requires a valid VCF and a trio definition, for example:

$ bcftools +mendelian file.vcf -- -t mother,father,child

Multiple trios can be tested at once by providing a list of trios:

$ bcftools +mendelian file.vcf -- -T trios.txt
$ cat trios.txt

The inconsistent genotypes can be deleted by setting to ./. (with the -d, --delete option), inconsistent sites can be counted (give the -c, --count option) or listed (the -l, --list option).

On output three values are printed for each trio

# [1]nOK  [2]nBad  [3]nSkipped  [4]Trio
334518    4621     996          mother,father,child


  • nOK .. number of genotypes at which the trio had no missingness and no Mendelian error

  • nBad .. number of genotypes at which the trio had a Mendelian error

  • nSkipped .. number of genotypes at which that trio had at least one individual missing and therefore could not be considered

The program takes the genotypes as they are, not considering genotype quality (FORMAT/GQ). If pre-filtering is desired, the plugin setGT can be used.


We welcome your feedback, please help us improve this page by either opening an issue on github or editing it directly and sending a pull request.