FIlter bam-file by chromosome and range

filter_bam_file.sh

#!/bin/bash

##############################
#set the following variables
##############################

#use the bamfile without .bam
myfile="alignment"
#the chromosome to filter for
mychrom="chr1"
# reads that start inbetween $from and $to get selected 
from="43500000"
to=  "43600000"
#how many reads should be in the resultfile at max
readnumber="50"

##############################
#script starts here
##############################

samfile="${myfile}.sam"
bamfile="${myfile}.bam"
samchromfile="${myfile}_${mychrom}".sam
samchromtargetfile="${myfile}_${mychrom}_from_${from}_to_${to}.sam"
bamchromtargetfile="${myfile}_${mychrom}_from_${from}_to_${to}.bam"
sortedbamchromtargetfile="${myfile}_${mychrom}_from_${from}_to_${to}_sorted.bam"
tmpfile="tmp.txt"

##convert initial bam to sam
samtools view -h "${bamfile}" > "${samfile}"
#filter by chromosome
cat ${samfile} | awk -v mychrom=${mychrom} 'BEGIN{FS="\t";} {if($3==mychrom) print $0}' > ${samchromfile}
#filter by given target (start and end)
cat ${samchromfile} | awk -v from=${from} -v to=${to} '{FS="\t"} $4>=from && $4<=to' from=$from to=$to > ${samchromtargetfile}
#take the first x lines
head -n ${readnumber} ${samchromtargetfile} > ${tmpfile} && mv ${tmpfile} ${samchromtargetfile}
#push the original header to the beginning of the new file
head -n 1000 ${samfile} | grep  "^@" | cat - ${samchromtargetfile} > ${tmpfile} && mv ${tmpfile} ${samchromtargetfile}

#convert sam to bam
samtools view -bS ${samchromtargetfile} > ${bamchromtargetfile}
tmpfilename=`echo "${sortedbamchromtargetfile}" | sed "s/.bam$//"`
# create sorted bam
samtools sort "${bamchromtargetfile}" "${tmpfilename}"
tmpfilename=`echo "${sortedbamchromtargetfile}" | sed "s/.bam$//"`
#create bai
samtools index "${sortedbamchromtargetfile}" "${tmpfilename}.bai"