Plugin mendelian2
This plugin is intended for detecting Mendelian inconsistencies. On input the program requires a valid VCF and a trio definition, for example:
$ bcftools +mendelian2 file.vcf -p child,father,mother
Multiple trios can be tested at once by providing a list of trios in ped format:
$ bcftools +mendelian file.vcf -P trios.ped $ cat trios.ped ignored boy father mother 1 ignored girl father mother 1
The inconsistent genotypes can be deleted by setting to ./. (with the -m d option),
inconsistent sites can be counted (-m c), listed (-m e), etc.
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.
The complete usage page obtained by bcftools +mendelian2 -h:
About: Count Mendelian consistent / inconsistent genotypes.
Usage: bcftools +mendelian2 [Options]
Common Options:
-e, --exclude EXPR Exclude sites for which the expression is true
-i, --include EXPR Include sites for which the expression is true
-o, --output FILE Output file name [stdout]
-O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]
-r, --regions REG Restrict to comma-separated list of regions
-R, --regions-file FILE Restrict to regions listed in a file
--regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]
-t, --targets REG Similar to -r but streams rather than index-jumps
-T, --targets-file FILE Similar to -R but streams rather than index-jumps
--targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]
--no-version Do not append version and command line to the header
-v, --verbosity INT Verbosity level
-W, --write-index[=FMT] Automatically index the output files [off]
Options:
-m, --mode c|[adeEgmMS] Output mode, the default is `-m c`. Multiple modes can be combined in VCF/BCF
output and the drop modes take precedence.
Text stats output:
c .. print counts, a text summary with the number of errors per trio
VCF/BCF output:
a .. add INFO/MERR annotation with the number of inconsistent trios
d .. delete genotypes in inconsistent trios (set to "./.")
e .. output sites with at least one erroneous trio
E .. drop sites with at least one erroneous trio
g .. output sites with at least one good trio (i.e. non-missing and consistent)
m .. output sites with missing genotypes in at least one trio
M .. drop sites with missing genotypes in at least one trio
S .. drop sites skipped for various reasons when collecting stats
-p, --pfm [1X:|2X:]P,F,M Sample names of child (the proband), father, mother; "1X:" for male pattern of chrX inheritance [2X:]
-P, --ped FILE PED file with the columns: <ignored>,proband,father,mother,sex(1:male,2:female)
--rules ASSEMBLY[?] Predefined inheritance rules, "list" to print available settings, "list?" for detailed information
--rules-file FILE Inheritance rules, run with `--rules list?` for examples
Example:
# Print number of good, erroneous and missing genotypes
bcftools +mendelian2 in.vcf -p 1X:Child,Father,Mother -m c
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