Vpeep - Revision history

Atks: /* Output */

2012-01-19T15:48:55Z

Output

← Older revision		Revision as of 11:48, 19 January 2012
Line 11:		Line 11:

	user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf		user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf
	~~atks@fantasia:~/data/cg$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf~~
	##fileformat=VCFv4.1		##fileformat=VCFv4.1
	##fileDate=20111105		##fileDate=20111105

Atks: /* Output */

2012-01-19T15:48:42Z

Output

← Older revision		Revision as of 11:48, 19 January 2012
Line 10:		Line 10:
	== Output ==		== Output ==

	user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf		user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf
	atks@fantasia:~/data/cg$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf		atks@fantasia:~/data/cg$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf
	##fileformat=VCFv4.1		##fileformat=VCFv4.1

Atks: /* Output */

2012-01-19T15:48:34Z

Output

← Older revision		Revision as of 11:48, 19 January 2012
Line 10:		Line 10:
	== Output ==		== Output ==

	user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf		user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf
	atks@fantasia:~/data/cg$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf		atks@fantasia:~/data/cg$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf
	##fileformat=VCFv4.1		##fileformat=VCFv4.1
	##fileDate=20111105		##fileDate=20111105

Atks: /* Output */

2012-01-19T15:48:20Z

Output

← Older revision		Revision as of 11:48, 19 January 2012
Line 11:		Line 11:

	user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf		user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf
	##fileformat=VCFv4.1		atks@fantasia:~/data/cg$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf
	##fileDate=20111105		##fileformat=VCFv4.1
	##source=CGA Tools v1.3 listvariants/testvariants		##fileDate=20111105
	##reference=/sup/sv-01/users/scordes/cgatools_files/build37.crr		##source=CGA Tools v1.3 listvariants/testvariants
	##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples with Fully Called Data">		##reference=/sup/sv-01/users/scordes/cgatools_files/build37.crr
	##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">		##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples with Fully Called Data">
	##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">		##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
	##INFO=<ID=RSID,Number=A,Type=String,Description="dbSNP rs ids">		##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
	##FILTER=<ID=s50,Description="Less than 50% of samples are fully called">		##INFO=<ID=RSID,Number=A,Type=String,Description="dbSNP rs ids">
	##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">		##FILTER=<ID=s50,Description="Less than 50% of samples are fully called">
	Genotype fields present: 69 individuals		##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
			Genotype fields present: 69 individuals
	No. of SNPs : 72798
	2 alleles : 12		No. of SNPs : 72798
	3 alleles : 72518		2 alleles : 12
	4 alleles : 268		3 alleles : 72518
	No. of MNPs : 490286		4 alleles : 268
	Length 2 : 297135		No. of MNPs : 490286
	Length 3 : 155284		Length 2 : 297135
	Length 4 : 21621		Length 3 : 155284
	Length >=5 : 16246		Length 4 : 21621
	No. of INDELs : 3905430		Length >=5 : 16246
	Insertions : 1837950		No. of INDELs : 3905430
	Deletions : 1931173		Insertions : 1837950
	Multiallelic : 136307		Deletions : 1931173
	No. of SVs : 2506		Multiallelic : 136307
	Precise : 2506		No. of SVs : 2506
	Unprecise : 0		Precise : 2506
	No. of CRs : 0		Unprecise : 0
	Total No. of Variants : 4471020		No. of CRs : 0
			Total No. of Variants : 4471020
	INDEL GALD - 1 to 50
	SV GALD - 51 to 194		INDEL GALD - 1 to 50
			SV GALD - 51 to 194
	SNP - Single Nucleotide Polymorphism
	MNP - Multiple Nucleotide Polymorphism		SNP - Single Nucleotide Polymorphism
	INDEL - Insertions and Deletions (GALD<=50)		MNP - Multiple Nucleotide Polymorphism
	SV - Structural Variants (GALD>50)		INDEL - Insertions and Deletions (GALD<=50)
	CR - Chromosomal Rearrangements		SV - Structural Variants (GALD>50)
			CR - Chromosomal Rearrangements
	GALD - Greatest Allele Length Difference
	defined as greatest length difference amongst all alleles		GALD - Greatest Allele Length Difference
	Precise - SV alternative allele denoted in the same way as INDELs		defined as greatest length difference amongst all alleles
	Unprecise - SV alternative allele denoted by <INS:ME:L1> for example		Precise - SV alternative allele denoted in the same way as INDELs
			Unprecise - SV alternative allele denoted by <INS:ME:L1> for example

	== Access ==		== Access ==

Atks: Created page with 'Category:Software '''vpeep''' checks the distribution in a VCF file. == Basic Usage Example == vpeep example: vpeep pscalare.vcf == Output == user…'

2012-01-19T15:47:42Z

Created page with 'Category:Software '''vpeep''' checks the distribution in a VCF file. == Basic Usage Example == vpeep <vcf-file> example: vpeep pscalare.vcf == Output == user…'

New page

[[Category:Software]]
'''vpeep''' checks the distribution in a VCF file.

== Basic Usage Example ==

vpeep <vcf-file>

example: vpeep pscalare.vcf

== Output ==

user@host:~$ vpeep CGI.public.69genomes.PASS.nonsnps.vcf
##fileformat=VCFv4.1
##fileDate=20111105
##source=CGA Tools v1.3 listvariants/testvariants
##reference=/sup/sv-01/users/scordes/cgatools_files/build37.crr
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples with Fully Called Data">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=RSID,Number=A,Type=String,Description="dbSNP rs ids">
##FILTER=<ID=s50,Description="Less than 50% of samples are fully called">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
Genotype fields present: 69 individuals

No. of SNPs : 72798
2 alleles : 12
3 alleles : 72518
4 alleles : 268
No. of MNPs : 490286
Length 2 : 297135
Length 3 : 155284
Length 4 : 21621
Length >=5 : 16246
No. of INDELs : 3905430
Insertions : 1837950
Deletions : 1931173
Multiallelic : 136307
No. of SVs : 2506
Precise : 2506
Unprecise : 0
No. of CRs : 0
Total No. of Variants : 4471020

INDEL GALD - 1 to 50
SV GALD - 51 to 194

SNP - Single Nucleotide Polymorphism
MNP - Multiple Nucleotide Polymorphism
INDEL - Insertions and Deletions (GALD<=50)
SV - Structural Variants (GALD>50)
CR - Chromosomal Rearrangements

GALD - Greatest Allele Length Difference
defined as greatest length difference amongst all alleles
Precise - SV alternative allele denoted in the same way as INDELs
Unprecise - SV alternative allele denoted by <INS:ME:L1> for example

== Access ==

Point to /net/fantasia/home/atks/programs/vtools for access to tools.

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