Difference between revisions of "Vmatch"
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For the current vmatch, please go to [sourceforge]. | For the current vmatch, please go to [sourceforge]. | ||
− | You will also need a copy of the memory mapped file: [http://www-personal.umich.edu/~atks/human.g1k.v37-bs.umfa.gz] | + | You will also need a copy of the memory mapped file: [http://www-personal.umich.edu/~atks/human.g1k.v37-bs.umfa.gz human.g1k.v37-bs.umfa]. Please gunzip it before usage. |
Revision as of 15:26, 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
user@host:~$ vmatch gatk.vcf samtools.vcf -w 10 -d
VCF file A : gatk.vcf VCF file B : samtools.vcf Genome file : 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
user@host:~$ 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 vmatch, please go to [sourceforge].
You will also need a copy of the memory mapped file: human.g1k.v37-bs.umfa. Please gunzip it before usage.