Perl script to check Mendelian errors in VCF file using pedigree information
$ perl check_mendel.pl --vcf [VCF] --ped [PED] --out [output_prefix]
- VCF file with GT field
- PED file with trio or duo information
- [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