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 to detect overlaps between variants
   d              debug option to generate a match.log file that gives all the matches made

Output

	    atks@fantasia:~/data/got2d$ vmatch got2d.wg4x.1511samples.73976indels.gatk.chr20.sites.vcf  got2d.wg4x.1514samples.71994indels.samtools.chr20.sites.vcf -w 10 -d  
   VCF file A  : got2d.wg4x.1511samples.73976indels.gatk.chr20.sites.vcf
   VCF file B  : got2d.wg4x.1514samples.71994indels.samtools.chr20.sites.vcf
   
   Genome file : /net/fantasia/home/atks/ref/genome/human.g1k.v37.fa
   Window Size : 10
   SRSA  : 8578
   SRSAN : 34522
   SRDA  : 2363
   SRDNA : 888
   DRDA  : 2322
   DRDNA : 439
   
   #A Records : 73976
   #B Records : 71994
   Match %tage for VCF file A
   Level 1 (SRSA, SRSAN)                          : 58.2621
   Level 2 (SRSA, SRSAN, SRDA, SRDNA)             : 62.6568
   Level 3 (SRSA, SRSAN, SRDA, SRDNA, DRDA, DRDNA): 66.3891
   Match %tage for VCF file B
   Level 1 (SRSA, SRSAN)                          : 59.8661
   Level 2 (SRSA, SRSAN, SRDA, SRDNA)             : 64.3818
   Level 3 (SRSA, SRSAN, SRDA, SRDNA, DRDA, DRDNA): 68.2168
   Matched variants written to match.txt
   Match logs written to match.log
   
   atks@fantasia:~/data/got2d$ head match.txt 
   id1 id2 match_type  extended_no_bases   normalized
   A4  B1  SRSAN   0   1
   A5  B2  SRSAN   0   1
   A6  B4  SRSA    0   0
   A7  B5  SRSAN   0   1
   A8  B6  SRSA    0   0
   A9  B7  SRDA    0   1
   A10 B8  SRSAN   0   1
   A11 B9  SRSAN   0   1
   A12 B10 SRSAN   0   1

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.