A script to do this would normally consist of two steps (irrespective of which programming language you use):

1. Read the input file and collect all data in key-value data structure (this would be called a hash table in Perl, a dictionary in Python, or an unordered map in C++). The key would be what is in column 1 and the value would be collecting all results pertaining to the key in question.
2. Iterate over all the (sorted) keys in the your key-value data structure and print out all the pairs to produce the output file.

Check out the "groupBy" command in my filo package. It is designed to handle exactly this problem. GroupBy only requires that 1) your input data be sorted by the columns that you want to group/consolidate, and 2), your data are tab-delimited. Here is an example with your data:

$ cat data.txt 
#Col1   Col2
Name1   AB, AC, CF
Name1   AF, AV, CG, HG
Name2   BB, BF, CD, CK, JK
Name2   BC

$ groupBy -i data.txt -grp 1 -opCols 2 -ops collapse
Name1   AB, AC, CF,AF, AV, CG, HG
Name2   BB, BF, CD, CK, JK,BC

Or, more briefly:

$ groupBy -i data.txt -g 1 -c 2 -o collapse
Name1   AB, AC, CF,AF, AV, CG, HG
Name2   BB, BF, CD, CK, JK,BC

Here are some other usage examples:

• Example 1
• Example 2
• Example 3

awk -F"t" '{if(NR==1){print} else hsh[$1]=hsh[$1]$2", "}END{for (i in hsh){print i" "hsh[i]}}' input_file | sed 's/, $//'

Output:

Col1    Col2
Name1 AB, AC, CF, AF, AV, CG, HG
Name2 BB, BF, CD, CK, JK, BC

Assuming the 2 columns separated by a tab, sample input file will be:

echo -e "Col1\tCol2
Name1\tAB, AC, CF
Name1\tAF, AV, CG, HG
Name2\tBB, BF, CD, CK, JK
Name2\tBC" > sample1

[?]

One-liner-solution:

cat sample1 | ruby -e 'c = Hash.new([]); while l = STDIN.gets; next if STDIN.lineno == 1; key, values = l.chomp.split "\t"; values = values.split ", "; c[key] += values; end; puts "Col1\tCol2"; c.each do |key, values|; vjoined=values.join ", "; puts "#{key}\t#{vjoined}"; end'

[?]

Output:

Col1    Col2
Name1   AB, AC, CF, AF, AV, CG, HG
Name2   BB, BF, CD, CK, JK, BC

[?]

The code in readable format (filename: consolidate.rb):

#!/usr/bin/env ruby

c = Hash.new []

while l = STDIN.gets
  next if STDIN.lineno == 1 # Cut the header off (first line)
  key, values = l.chomp.split "\t" 
  values = values.split ", "
  c[key] += values
end

puts "Col1\tCol2"
c.each do |key, values|
  puts "#{key}\t#{values.join ', '}"
end

! /usr/bin/perl -w

use strict;

open (F, "file") || die "cannot open file" ; #file has data in two tab-delimited columns.

my %hoa; # a hash of arrays.

while (<F>){
   chomp;
   my @line = split/\t/;
   push (@{$hoa{$line[0]}}, $line[1]);
}

foreach my $k (sort keys %hoa){
   my $data = join(",", @{$hoa{$k}});
   print("$k\t$data\n");
}
#amen.

have not checked script...but you get the idea.