vcf

addAncAllele2Ref.py

Create an ancestral fasta file from a reference by replacing the ref base with the ancestral base. Requires Biopython. Ancestral file format has 3 columns CHROM POS ALLELE

chunkvcf.py

breaks vcf into smaller chunks for faster processing chunkvcf.py --vcf FOO.vcf --integer 10000

derivedVCF.py

creates a VCF with polarization defined by est-sfs (Keightly and Jackson 2018)

estsfs_format.py

Create input files for est-sfs (Keightly and Jackson 2018) file format should be from vcftools --counts estsfs_format.py -i ingroup.counts -o1 outgroup.counts [-o2 outgroup.counts -o3 outgroup.counts]

fb2gatk.py

convert freebayes vcf format to that used by gatk

fixfbmiss.py

fixes freebayes missing to be in the same format as gatk

fixgtfieldlength.py

The fields can be different lengths if the site is physically phased in gatk

fixmissing.py

reformats missing sites in VCf

gatknorm.py

normalizes a gatk file for merging

geno2vcf.py

creates a geno file (Plink) from a vcf

normgatkfields.py

normalizes gatk fior merging

vcf2bedgraph.py

create a bedgraph from a vcf file

vcf2fasta_consensus.py

This program creates a consensus fasta sequence, new reference, that uses information from a population vcf to replace the reference base with fixed or high freq ALT calls

vcf2linkSelThin.py

thin a vcf file to reduce the effects of linked selection.

vcf2sample_resort.py

remake the header for a vcf

vcf_fill_gvcf.py

fill a gvcf file with 0 band