Vmatch - Revision history

Atks: /* Download */

2012-01-23T21:11:35Z

Download

← Older revision		Revision as of 17:11, 23 January 2012
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	[http://www-personal.umich.edu/~atks/vmatch vmatch 0.5]		[http://www-personal.umich.edu/~atks/vmatch vmatch 0.5]

	You will also need a copy of human genome assembly fasta file: [http://www-personal.umich.edu/~atks/human.g1k.v37.fa.gz human.g1k.v37.fa]. Please gunzip it before usage. arf will generate a memory mapped file from ~~these~~ fasta file human.g1k.v37-bs.umfa.		You will also need a copy of human genome assembly fasta file: [http://www-personal.umich.edu/~atks/human.g1k.v37.fa.gz human.g1k.v37.fa]. Please gunzip it before usage. arf will generate a memory mapped file from the fasta file named human.g1k.v37-bs.umfa.

	This page is maintained by [mailto:atks@umich.edu Adrian].		This page is maintained by [mailto:atks@umich.edu Adrian].

2012-01-23T20:58:02Z

Download

← Older revision		Revision as of 16:58, 23 January 2012
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	[http://www-personal.umich.edu/~atks/vmatch vmatch 0.5]		[http://www-personal.umich.edu/~atks/vmatch vmatch 0.5]

	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. ~~Note that to use it, please refer to the~~ file ~~as human.g1k.v37.fa, it will be automatically renamed as~~ human.g1k.v37-bs.umfa ~~by vmatch~~.		You will also need a copy of human genome assembly fasta file: [http://www-personal.umich.edu/~atks/human.g1k.v37.fa.gz human.g1k.v37.fa]. Please gunzip it before usage. arf will generate a memory mapped file from these fasta file human.g1k.v37-bs.umfa.

	This page is maintained by [mailto:atks@umich.edu Adrian].		This page is maintained by [mailto:atks@umich.edu Adrian].

2012-01-17T22:37:12Z

Download

← Older revision		Revision as of 18:37, 17 January 2012
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	For vmatch 0.5, we provide binaries for linux machines.		For vmatch 0.5, we provide binaries for linux machines.
			[http://www-personal.umich.edu/~atks/vmatch vmatch 0.5]

	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. Note that to use it, please refer to the file as human.g1k.v37.fa, it will be automatically renamed as human.g1k.v37-bs.umfa by vmatch.		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. Note that to use it, please refer to the file as human.g1k.v37.fa, it will be automatically renamed as human.g1k.v37-bs.umfa by vmatch.

	This page is maintained by [mailto:atks@umich.edu Adrian].		This page is maintained by [mailto:atks@umich.edu Adrian].

2012-01-16T20:42:45Z

Output

← Older revision		Revision as of 16:42, 16 January 2012
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	#match_type denotes the match classification per match pair		#match_type denotes the match classification per match pair
	#extended_no_of_bases is the number of bases extended in the extension step		#extended_no_of_bases is the number of bases extended in the extension step
	#normalized is is a binary stating whether normalization resulted in a more		#normalized is a binary stating whether normalization resulted in a more
	#parsimonious representation of the alleles		#parsimonious representation of the alleles
	#these fields allows one to look for certain signatures in matches that one might		#these fields allows one to look for certain signatures in matches that one might

2012-01-16T20:01:49Z

Output

2012-01-16T20:00:40Z

Output

@@ Line 75: / Line 75: @@
      A11 B9  SRSAN   0   1
      A12 B10 SRSAN   0   1
 == Description ==

2012-01-16T19:48:30Z

Command Line Options

← Older revision		Revision as of 15:48, 16 January 2012
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	vcf-file-1 VCF file (can be gzipped or bgzipped)		vcf-file-1 VCF file (can be gzipped or bgzipped)
	vcf-file-2 VCF file (can be gzipped or bgzipped)		vcf-file-2 VCF file (can be gzipped or bgzipped)
	genome-file Memory Mapped Sequence file		genome-file Memory Mapped Sequence file
			(note that if genome.fa is specified, the actual file looked for is genome-bs.umfa)
	w window size to detect overlaps between variants		w window size to detect overlaps between variants
	d debug option to generate a match.log file that gives all the matches made		d debug option to generate a match.log file that gives all the matches made

2012-01-16T19:46:44Z

Output

← Older revision		Revision as of 15:46, 16 January 2012
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	== Output ==		== Output ==

	user@host:~$ vmatch gatk.vcf samtools.vcf -w 10 -d		user@host:~$ vmatch gatk.vcf samtools.vcf -w 10 -d

2012-01-16T19:45:53Z

Output

← Older revision		Revision as of 15:45, 16 January 2012
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	#matching classifications after extension and normalizaiton		#matching classifications after extension and normalizaiton
	#SRSA : Same REF Same ALT without normalization		#SRSA : Same REF Same ALT without normalization
	#SRSAN: Same REF Same ALT only after normalization		#SRSAN : Same REF Same ALT only after normalization
	#SRDA : Same REF Different ALT		#SRDA : Same REF Different ALT
	#SRDNA : Same REF Different Number ALT		#SRDNA : Same REF Different Number ALT

2012-01-16T19:45:36Z

Output

← Older revision		Revision as of 15:45, 16 January 2012
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	Match logs written to match.log		Match logs written to match.log

	#matching classifications		#matching classifications after extension and normalizaiton
	#SRSA : Same REF Same ALT		#SRSA : Same REF Same ALT without normalization
			#SRSAN: Same REF Same ALT only after normalization
	#SRDA : Same REF Different ALT		#SRDA : Same REF Different ALT
	#SRDNA : Same REF Different Number ALT		#SRDNA : Same REF Different Number ALT