chomp;
        my @line = split /\s+/, $_;
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That is usually written as:

        my @line = split;
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            if ($bwa{$ID}[2] =~ /[D]/) { $splitstoreD = 1; } else { $s
+plitstoreD = 0 }
            if ($bwa{$ID}[2] =~ /[I]/) { $splitstoreI = 1; } else { $s
+plitstoreI = 0 }
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That is usually written as:

            $splitstoreD = $bwa{$ID}[2] =~ /D/ ? 1 : 0;
            $splitstoreI = $bwa{$ID}[2] =~ /I/ ? 1 : 0;
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Or simply:

            $splitstoreD = $bwa{$ID}[2] =~ /D/;
            $splitstoreI = $bwa{$ID}[2] =~ /I/;
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            #Defining Deletions
            if($splitstoreD == 1) { $bwa{$ID}[11]="Del" } else { $bwa{
+$ID}[11]=0 }
            
            #Defining Insertions
            if($splitstoreI == 1) { $bwa{$ID}[12]="Ins" } else { $bwa{
+$ID}[12]=0 }
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That is usually written as:

            #Defining Deletions
            $bwa{$ID}[11] = $splitstoreD == 1 ? 'Del' :0;

            #Defining Insertions
            $bwa{$ID}[12] = $splitstoreI == 1 ? 'Ins' : 0;
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                @s2 = split /(\d+M)/, @s1;
                @s3 = split /(\d+M)/, @s2;
                @s4 = split /(\d+I)/, @s3;
                @s5 = split /[D]/, @s4;
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You are using an array in scalar context which means that if @s1 has 53 elements, for example, then @s2 = split /(\d+M)/, @s1 is the same as @s2 = split /(\d+M)/, '53'.    The second argument to split has to be a scalar or it will be evaluated as a scalar.