diff --git a/03.selection_signature/XP-EHH/XP-EHH.sh b/03.selection_signature/XP-EHH/XP-EHH.sh index d4c4f2d..84c77c3 100644 --- a/03.selection_signature/XP-EHH/XP-EHH.sh +++ b/03.selection_signature/XP-EHH/XP-EHH.sh @@ -65,28 +65,28 @@ function main() { mkdir XP-EHH.progress -#extract sample +# extract sample $vcftools --gzvcf $vcf --keep $ref --recode --recode-INFO-all --out ./XP-EHH.progress/01.ref $vcftools --gzvcf $vcf --keep $tag --recode --recode-INFO-all --out ./XP-EHH.progress/01.tag cd XP-EHH.progress for ((k=1; k<=$chr; k++)); do -#splite chr for ref and tag +# splite chr for ref and tag $vcftools --vcf 01.ref.recode.vcf --recode --recode-INFO-all --chr ${k} --out ref.chr${k} $vcftools --vcf 01.tag.recode.vcf --recode --recode-INFO-all --chr ${k} --out tag.chr${k} -#calculate map distance +# calculate map distance $vcftools --vcf ref.chr${k}.recode.vcf --plink --out chr${k}.MT awk 'BEGIN{OFS=" "} {print 1,".",$4/1000000,$4}' chr${k}.MT.map > chr${k}.MT.map.distance done for ((k=1; k<=$chr; k++)); do -#XP-EHH +# XP-EHH $selscan --xpehh --vcf tag.chr${k}.recode.vcf --vcf-ref ref.chr${k}.recode.vcf --map chr${k}.MT.map.distance --threads $thread --out chr${k}.ref_tag -#norm +# norm $norm --xpehh --files chr${k}.ref_tag.xpehh.out --bp-win --winsize $win -#加窗口步长 +# add win and step python ../XPEHH_Win_step.py --file chr${k}.ref_tag.xpehh.out.norm --chr $k --window $win --step $step done cat {1.."$chr"}.XPEHH > ../${output}.XPEHH