Scripts to perform various bioinformatics operations. These are generally written in Python, but I use whatever language is most apropriate.
tassel2fastPHASE.py converts a TASSEL hapmap file to a fastPHASE input file.
fastPHASE2tassel.py converts a fastPHASE output file to a TASSEL hapmap file. It
requires the original TASSEL hapmap file used to convert to fastPHASE input.
fastPHASE2vcf.py converts the output of fastPHASE to a VCF. It requires
the output from fastPHASE (i.e. "switch_guess") and an original VCF file that
was used to convert to fastPHASE input (PLINK has a setting to convert a VCF
to fastPHASE input). If the low genotype likelihood setting was used in
fastPHASE, those genotypes will be set to missing.
vcf2hapmap.py converts a VCF to a hapmap file that is either suitable for
TASSEL or suitable for the rrBLUP R package.
LB_impute_vcf_prep.py filters and prepared VCF files for used in the imputation
program LB-Impute. It requires
a VCF and a pedigree file. The program first filters parents based on markers that
are homozygous within parents and polymorphic between parents. The program then
evaluates progeny for degree of missingness.