Difference between revisions of "Vmatch"
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vcf-file VCF file | vcf-file VCF file | ||
genome-file Memory Mapped Sequence file | genome-file Memory Mapped Sequence file | ||
− | w window size | + | w window size to detect overlaps between variants |
− | d debug | + | d debug option to generate a match.log file that gives all the matches made |
== Output == | == Output == |
Revision as of 11:13, 16 January 2012
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
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.