#!/bin/bash
Plot the coverage script
chr=$1
start=$2
end=$3
samtools depth deduped_MA605.bam > deduped_MA605.coverage
awk '$1 == $chr {print $0}' deduped_MA605.coverage > chr1_MA605.coverage
#awk '$1 == 2 {print $0}' deduped_MA605.coverage > chr2_MA605.coverage
#Rscript
library(reshape)
my.chr2 <- read.table("my.coverage", header=FALSE, sep="\t", na.strings="NA", dec=".", strip.white=TRUE)`
my.chr2<-rename(my.chr2,c(V1="Chr", V2="locus", V3="depth")) # renames the header
plot(my.chr2$locus, my.chr2$depth)
#Shushi tool .... gawk '{/^[0-9]/{print >$1".coverag"}' ./deduped_MA605.coverag
