Vmatch

vmatch is a variant matching program for MNPs, INDELs and precise SVs in VCF files.

Basic Usage Example

 vmatch <vcf-file-1> <vcf-file-2> -g <genome-file> -w <int> -d

Here is an example of how vmatch works:

  vmatch 1000g.vcf got2d.vcf -g hg18.fa  -w 10 -d

Command Line Options

   vcf-file       VCF file
   genome-file    Memory Mapped Sequence file
   w              window size
   d              debug

Description

   Outputs 2 files
     match.txt : gives the matched pairs
                 1)id1
                 2)id2
                 3)match type
                 4)extended no of bases
                 5)normalized
     match.log : Details of the extension and normalization process for all compared pairs
   vmatch matches the variants in 2 VCF files by choosing the best match for every
   possible variant pair.  The percentage of matches is given at 3 levels for each
   variant total of both VCF files.

   The 3 match levels (in order of decreasing strictness) are given as:
      Level 1) SRSA    - Same Position, same REF and ALT
      Level 1) SRSAN   - Same Position, same REF and ALT after normalization
      Level 2) SRDA    - Same Position, same REF and different ALT
      Level 2) SRDNA   - Same Position, same REF and different number of ALT
      Level 3) DRDA    - Same Position, different REF and different ALT
      Level 3) DRDNA   - Same Position, different REF and different number of ALT
 
      Level 1 represents matches in position and alleles
      Level 2 represents matches in position and reference alleles but different alternate alleles
      Level 3 represents matches only in position

Download

For the current lfSingle, please go to our GLF Tools Website.

TODO

Support for X chromosome variant calling.

Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.