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[[Category:Software]]
'''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 <code>vmatch</code> 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 [http://www.sph.umich.edu/csg/abecasis/glfTools/ 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.
'''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 <code>vmatch</code> 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 [http://www.sph.umich.edu/csg/abecasis/glfTools/ 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.
