Entering edit mode
7 months ago
I attempt to do a selective sweep analysis by using the software XP-CLR1.0. My genotypic data is VCF format so wonder if someone with experience on this package could recommend any tool to convert from VCF to the input file format required by this software?
Input files are:
geno file: contains the genotype of a single SNP, for example:
1 0 1 1 9 9
1 1 1 0 0 0
It contains two SNPs (rows) from three individuals (columns). First two columns are the two alleles of individual #1. Values 1 and 0 correspond to two allele types. 9 denotes missing data.
snp file: each row contains information of each SNP, for example:
snp_name, chr#, genetic_distance(cM), Physical_distance, Ref_allele, Alt_allele
