标签：LD && pos start chr awk peak snp block
#!/bin/bash
#LD PLOT
#author lee
echo"par1 is vcf,par2 is top_chr"
Genome=/public/home/caisl/lee/genome/rice/msu.gff3
while read chr pos
do
pos_up=$((pos-20000))
pos_down=$((pos+20000))
region=$chr":"$pos_up":"$pos_down
LDBlockShow -InVCF $1 -OutPut ${chr}_${pos} -Region $region -InGFF $Genome -OutPng -SeleVar 2 -TopSite
gunzip ${chr}_${pos}.blocks.gz
grep $pos ${chr}_${pos}.blocks|awk '{print}'>${chr}_${pos}_block
start=$(awk '{print $2}' ${chr}_${pos}_block)
end=$(awk '{print $3}' ${chr}_${pos}_block)
awk -v chr=$chr -v start=$start -v end=$end '{if($3=="gene" && $1==chr && $4>=start && $4<=end)print $0}' $Genome>${chr}_${pos}_block_gene;
done<$2
标签：LD,
&&,
pos,
start,
chr,
awk,
peak,
snp,
block
From： https://www.cnblogs.com/xiaosagege/p/16615775.html