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CHROM POS  REF ALT VARIANT_LIST 209T-D 459T-D 644T-D 94T-D 99T1-D 99T2
+-D 99T3-D 99T4-D 99T5-D
MT    1010 G   A   A            REF    A      A      REF   A      A   
+   A      A      A
MT    2962 C   T   T            REF    T      T      T     T      T   
+   T      T      T

CHROM POS  REF ALT VARIANT_LIST 209H-D 459H-D 644H-D 94H-D 99H-D
MT    1010 G   A   A            REF    REF    REF    REF   REF
MT    2962 C   T   T            REF    REF    T      REF   T

#! perl
use strict;
...

close $in1
    or die "Cannot close file '$file1': $!";

23:33 >perl 959b_SoPW.pl
CHROM POS  REF ALT VARIANT_LIST 209T-D 459T-D 644T-D 94T-D 99T1-D 99T2
+-D 99T3-D 99T4-D 99T5-D
...
MT 2962 C T T REF T REF T REF REF REF REF REF

23:33 >