We'll want to convert all of the VCFs to fasta format for the analysis of population recombination rate. Many programs (e.g., LDJump, LDhelmet) accept Fasta files as input.
Since SLiM VCFs are all As and Ts, we'll sample a section of Chlamydomonas genome of the same length as the genomic elements in SLiM. We'll then use a mutation matrix to overlay the substitution onto the chlamy reference sequence at positions specified in the VCF.
We'll want to convert all of the VCFs to fasta format for the analysis of population recombination rate. Many programs (e.g., LDJump, LDhelmet) accept Fasta files as input.
Since SLiM VCFs are all As and Ts, we'll sample a section of Chlamydomonas genome of the same length as the genomic elements in SLiM. We'll then use a mutation matrix to overlay the substitution onto the chlamy reference sequence at positions specified in the VCF.