/checkMendel

Perl script to check Mendelian errors in VCF file using pedigree information

Primary LanguagePerl

check_mendel.pl

Perl script to check Mendelian errors in VCF file using pedigree information

Usage

$ perl check_mendel.pl --vcf [VCF] --ped [PED] --out [output_prefix]

Input

  • VCF file with GT field
  • PED file with trio or duo information

Output

  • [output_prefix].tbl : A table with Mendelian error counts for all possible parent/child genotype combinations
  • [output_prefix].AC : Number of errors and variants for each allele count bin
  • [output_prefix].var : List of all variants with number of Mendelian errors annotated