Difference between revisions of "Vmatch"
From Genome Analysis Wiki
Jump to navigationJump to search (Created page with '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>…') |
|||
| Line 30: | Line 30: | ||
possible variant pair. The percentage of matches is given at 3 levels for each | possible variant pair. The percentage of matches is given at 3 levels for each | ||
variant total of both VCF files. | variant total of both VCF files. | ||
| + | |||
The 3 match levels (in order of decreasing strictness) are given as: | The 3 match levels (in order of decreasing strictness) are given as: | ||
Level 1) SRSA - Same Position, same REF and ALT | Level 1) SRSA - Same Position, same REF and ALT | ||
| Line 37: | Line 38: | ||
Level 3) DRDA - Same Position, different REF and different ALT | Level 3) DRDA - Same Position, different REF and different ALT | ||
Level 3) DRDNA - Same Position, different REF and different number of ALT | Level 3) DRDNA - Same Position, different REF and different number of ALT | ||
| + | |||
Level 1 represents matches in position and alleles | Level 1 represents matches in position and alleles | ||
Level 2 represents matches in position and reference alleles but different alternate alleles | Level 2 represents matches in position and reference alleles but different alternate alleles | ||
Revision as of 11:05, 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 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.
