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 mother1,father1,child1 mother2,father2,child2
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
where
-
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.
Feedback
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