SIgenesVCFfiltering

##Filter VCF by SI bed file

bcftools view -I -O z Schil_capture_variants_Chr1-12.reheader.filtered.vcf.gz \
-R ../bedFiles/selfincompatibility_genes1.bed -o Schil_capture_variants_Chr1-12.reheader.filtered.SIgenes.vcf.gz

##Filter VCF for unlinked SNPs

vcftools --gzvcf Schil_capture_variants_Chr1-12.reheader.filtered.SIgenes.vcf.gz --thin 200 --remove-indels --maf 0.05 \
--minDP 10 --max-missing 0.9 --out SIgenesSNPs --recode-INFO-all --recode

##PLINK LD pruning r² of 0.5

plink --vcf SIgenesSNPs.recode.vcf --indep-pairwise 50 5 0.5 --const-fid --allow-extra-chr \
--recode vcf --out pruned.SIgenesSNPs --set-missing-var-ids @:#

##Remove outgroups

bcftools view -s ^0_Spenn_LA0716_ERR418107,\
0_S.chiCGN15532_1_ERR418097,\
0_S.chiCGN15530_1_ERR418098,\
0_Sper_LA1278_ERR418084,\
0_Sper_LA1954_ERR418094 pruned.SIgenesSNPs.vcf > pruned.SIgenesSNPs.noOutgroup.vcf

## Edit VCF header to simplify sample names for visualization

bcftools query -l pruned.SIgenesSNPs.noOutgroup.vcf > sampleIDlist.txt

#Edit txt in VIM

%s/\(0_\)\(.*\)/\1\2\t\2/

#Reheader in VCF

bcftools reheader -s sampleIDlist.txt -o pruned.SIgenesSNPs.noOutgroup.rename.vcf pruned.SIgenesSNPs.noOutgroup.vcf

##Define populations for PGDSpider

sed -r 's/(.*)_.*/&\t\1/' allSampleNames.txt > populationDefinitions.txt