Shell Programming and Scripting

 add2text() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s\n," $id
		cd 'C:\Users\cmccabe\Desktop\annovar'
		while read line; do echo -e "$line\n"; done < file.txt
    esac 
}

 _matched.avinput

 #!/bin/bash
menu() {
    printf "\n MENU \n
    ==================================\n\n
    \t 1  Match patient\n
    \t 2  Sanger analysis\n
    \t 3  Batch analysis\n
    \t 4  Individual analysis\n
    \t 5  Supplemental analysis\n
    \t 6  Exit\n\n
    ==================================\n\n"
    printf "\t Your choice: "; read menu_choice
    case "$menu_choice" in
        1) match ;;
  2) sanger ;;
  3) batch ;;
  4) individual ;;
  5) supplemental ;;
        6) printf "\n Bye! \n\n"; exit ;;
        *) printf "\n Invalid choice."; sleep 2; menu ;;
    esac
}
match() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
    printf "What is the id of the patient to be matched  : "; read id
    printf "What panel: "; read panel
    [ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && menu
    [ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && menu
    cd 'C:\Users\cmccabe\Desktop\annovar'
    OMR=Output_Mutation_Report
    perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$p=join("\t",(split/\t/)[4,5]);($p,$_)} <>;$m{"#CHROM\tINFO"}=$m{"Chr\tSegment Position"}};/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next;$p=$F[0]."\t".$1;exists $m{$p} and print join("\t",$_,$m{$p})' ${id}_${panel}_${OMR}.txt < ${id}_${panel}_${OMR}_Filtered.vcf > ${id}_matched.vcf
    convert
}
convert() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
    printf "Does the file need to be converted? Y/N "; read convert_choice
    
    case "$convert_choice" in
        [yY]) perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput
        additional ;;
        [nN]) additional ;;  
        *) convert ;;
    esac
}
add2text() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
  cd 'C:\Users\cmccabe\Desktop\annovar'
  while read line; do echo -e "$line\n"; done < file.txt
    esac
}
additional() {
    printf "\n\n"
    printf "Are there additonal patients to be matched?  Y/N "; read match_choice
    case "$match_choice" in
        [yY]) id=""; panel=""; match ;;
        [nN]) id=""; panel=""; menu ;;  
        *) additional ;;
    esac
}
sanger() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s\n" $id
    printf "What is the name of the patient to have sanger annotation  : "; read id
    [ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && menu
    [ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && menu
    cd 'C:\Users\cmccabe\Desktop\annovar'
              $( perl table_annovar.pl ${id}.txt humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo )
    additionalsanger
}
additionalsanger() {
    printf "\n\n"
    printf "Are there additonal sanger patients?  Y/N "; read match_choice
    case "$match_choice" in
        [yY]) id="";  sanger ;;
        [nN]) id=""; panel=""; menu ;;  
        *) additional ;;
    esac
}
batch() {
    printf "\n\n"
    printf "How many patients  : "; read id
    [ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && menu
    [ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && menu
    cd 'C:\Users\cmccabe\Desktop\annovar'
              $( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt )
     printf "Are there additional patients  : "; read id
  case "$match_choice" in
        [yY]) id=""; individual ;;
        [nN]) id=""; panel=""; menu ;;
  *) individual ;;
    esac
}
individual() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
    printf "What is the id of the patient  : "; read id
    printf "What panel: "; read panel
    [ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && menu
    [ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && menu
    cd 'C:\Users\cmccabe\Desktop\annovar'
              $( perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo )
    printf "Are there additional patients  : "; read id
  case "$match_choice" in
        [yY]) id="";  individual ;;
        [nN]) id=""; panel=""; menu ;;
  *) additional ;;
    esac
}
supplemental() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
    printf "What is the id of the patient  : "; read id
    printf "What panel: "; read panel
    [ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && menu
    [ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && menu
    cd 'C:\Users\cmccabe\Desktop\annovar'
              $( perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,exac02,1000g2014oct_all,KAT6B,SPRED1,NF1 -operation g,f,f,f,f,f,f -otherinfo )
    printf "Are there additional patients  : "; read id
  case "$match_choice" in
        [yY]) id="";  individual ;;
        [nN]) id=""; panel=""; menu ;;
  *) additional ;;
    esac
}
# actual start of this program
menu # run menu function

 The id is the read id variable in the match section and the _matched.avinput comes from the convert section

 cat filename

 where 12345 and 67890 were inputted by the user in the matched script and the _matched.avinput resulted from the convert.