VcfCodingSnps - Revision history

Ppwhite at 15:58, 2 February 2017

2017-02-02T15:58:32Z

← Older revision		Revision as of 11:58, 2 February 2017
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	'''vcfCodingSnps'''[http://~~www~~.sph.umich.edu/~~csg~~/liyanmin/vcfCodingSnps/index.shtml] is a SNP annotation tool that annotates coding variants in a [[VCF]] format input file. It takes a VCF as input and generates an annotated VCF file as output. The tool is currently under development by Yanming Li, a doctoral student at the University of Michigan Center for Statistical Genetics. For any issues with the program, please contact [mailto:liyanmin@umich.edu Yanming]. A detailed tutorial and download page can be found at [http://~~www~~.sph.umich.edu/~~csg~~/liyanmin/vcfCodingSnps/index.shtml]		'''vcfCodingSnps'''[http://csg.sph.umich.edu//liyanmin/vcfCodingSnps/index.shtml] is a SNP annotation tool that annotates coding variants in a [[VCF]] format input file. It takes a VCF as input and generates an annotated VCF file as output. The tool is currently under development by Yanming Li, a doctoral student at the University of Michigan Center for Statistical Genetics. For any issues with the program, please contact [mailto:liyanmin@umich.edu Yanming]. A detailed tutorial and download page can be found at [http://csg.sph.umich.edu//liyanmin/vcfCodingSnps/index.shtml]

	== Basic Usage Example ==		== Basic Usage Example ==

Liyanmin at 06:28, 13 December 2010

2010-12-13T06:28:02Z

← Older revision		Revision as of 02:28, 13 December 2010
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	string symbol; "Standard gene symbol"		string symbol; "Standard gene symbol"

	Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R" etc. If a genelist downloaded by you own that does not contain such a field, you can simply make the 11th field equal to the first field which is the gene name in a specific track by a syntax like		Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R" etc.
			If a genelist downloaded by you own that does not contain such a field, you can simply make the 11th field equal to the first field which is the gene name in a specific track by a syntax like

	awk `{FS="\t"; print $0"\t"$1 }` yourGenelist > yourNewGenelist		awk `{FS="\t"; print $0"\t"$1 }` yourGenelist > yourNewGenelist

Liyanmin at 06:26, 13 December 2010

2010-12-13T06:26:28Z

← Older revision		Revision as of 02:26, 13 December 2010
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	uint[exonCount] exonEnds; "Exon end positions"		uint[exonCount] exonEnds; "Exon end positions"
	string symbol; "Standard gene symbol"		string symbol; "Standard gene symbol"
	Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R" etc. If a genelist downloaded by you own that does not contain such a field, you can simply make the 11th field equal to the first field which is the gene name in a specific track by a syntax like
	awk `{FS="\t"; print $0"\t"$1 }` yourGenelist > yourNewGenelist		Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R" etc. If a genelist downloaded by you own that does not contain such a field, you can simply make the 11th field equal to the first field which is the gene name in a specific track by a syntax like

			awk `{FS="\t"; print $0"\t"$1 }` yourGenelist > yourNewGenelist

	2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other		2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other
	reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is		reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is

Liyanmin at 06:25, 13 December 2010

2010-12-13T06:25:31Z

← Older revision		Revision as of 02:25, 13 December 2010
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	uint[exonCount] exonEnds; "Exon end positions"		uint[exonCount] exonEnds; "Exon end positions"
	string symbol; "Standard gene symbol"		string symbol; "Standard gene symbol"

	Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R" etc. If a genelist downloaded by you own that does not contain such a field, you can simply make the 11th field equal to the first field which is the gene name in a specific track by a syntax like		Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R" etc. If a genelist downloaded by you own that does not contain such a field, you can simply make the 11th field equal to the first field which is the gene name in a specific track by a syntax like
			awk `{FS="\t"; print $0"\t"$1 }` yourGenelist > yourNewGenelist
	awk `{FS="\t"; print $0"\t"$1 }` yourGenelist > yourNewGenelist

	2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other		2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other
	reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is		reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is

Liyanmin at 06:24, 13 December 2010

2010-12-13T06:24:58Z

← Older revision		Revision as of 02:24, 13 December 2010
Line 63:		Line 63:
	string symbol; "Standard gene symbol"		string symbol; "Standard gene symbol"

	Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R" etc. If a genelist downloaded by you own that does not contain such a field, you can simply make the 11th field equal to the first field which is the gene name in a specific track by a syntax like		Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R" etc. If a genelist downloaded by you own that does not contain such a field, you can simply make the 11th field equal to the first field which is the gene name in a specific track by a syntax like

	awk `{FS="\t"; print $0"\t"$1 }` yourGenelist > yourNewGenelist		awk `{FS="\t"; print $0"\t"$1 }` yourGenelist > yourNewGenelist

	2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other		2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other

Liyanmin at 06:24, 13 December 2010

2010-12-13T06:24:02Z

← Older revision		Revision as of 02:24, 13 December 2010
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	Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file		Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file

	1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 11 fields are required and must be of the same order as shown below:		1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 11 tab delimited fields are required and must be of the same order as shown below:
	string name; "Name of gene"		string name; "Name of gene"
	string chrom; "Chromosome name"		string chrom; "Chromosome name"
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	string symbol; "Standard gene symbol"		string symbol; "Standard gene symbol"

	Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R"		Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R" etc. If a genelist downloaded by you own that does not contain such a field, you can simply make the 11th field equal to the first field which is the gene name in a specific track by a syntax like

			awk `{FS="\t"; print $0"\t"$1 }` yourGenelist > yourNewGenelist

	2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other		2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other

Liyanmin at 06:17, 13 December 2010

2010-12-13T06:17:58Z

← Older revision		Revision as of 02:17, 13 December 2010
Line 62:		Line 62:
	uint[exonCount] exonEnds; "Exon end positions"		uint[exonCount] exonEnds; "Exon end positions"
	string symbol; "Standard gene symbol"		string symbol; "Standard gene symbol"

			Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R"

	2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other		2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other

Liyanmin at 06:07, 13 December 2010

2010-12-13T06:07:46Z

← Older revision		Revision as of 02:07, 13 December 2010
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	2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other		2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other
	reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is		reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is
	not a multiple of three". While we will use the usual mod 3 method for counting codons.		not a multiple of three". While we will use the usual mod 3 method for counting codons.
	3. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables].		3. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables].
	4. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570).		4. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570).

Liyanmin at 06:06, 13 December 2010

2010-12-13T06:06:48Z

← Older revision		Revision as of 02:06, 13 December 2010
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	--ns parameter user defined number of kbps for the range of upstream or downstream of a gene, by default will be set t0 5		--ns parameter user defined number of kbps for the range of upstream or downstream of a gene, by default will be set t0 5

	== Library Compiling Guideline ==		== Library Compiling Guideline ==

	To Compile the source code, please first re-compile the .c functions in the library folder on your local machine:		To Compile the source code, please first re-compile the .c functions in the library folder on your local machine:
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	... ...		... ...

	2. Input gene file should be a plain text file generated by [http://genome.ucsc.edu/ ucsc genome browser]. A sample pathway of generating an input gene file is		2. The gene list and the reference genome that user provided can be of various gene tracks and assemblies. The latest version takes gene list tracks such as UCSC known genes, RefSeq genes, Genecode genes, CCDS genes and Emsembl genes, and the assembly of the gene list and the reference genome can be of either hg16, hg17, hg18 or hg19. One can explore UCSC genome browser for a better understanding of different tracks and assemblies. By default vcfColdingSnps uses a hg18 UCSC known gene list and the hg18 reference genome. It also provides versions of other tracks and assemblies at the user's conveinience so that they don't need to download those themselves. Input gene file should be a plain text file generated by [http://genome.ucsc.edu/ ucsc genome browser]. A sample pathway of generating an input gene file is

	Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file		Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file
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	uint[exonCount] exonEnds; "Exon end positions"		uint[exonCount] exonEnds; "Exon end positions"
	string symbol; "Standard gene symbol"		string symbol; "Standard gene symbol"
	~~Note:~~
	2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other		2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other
	reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is		reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is
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	8 152578 . c t 87 . depth=108;5'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=RPL23A_20_869(uc010lrb.1)[-] GT:GQ:GD 1/1:95:31 1/1:89:30 1/1:100:47		8 152578 . c t 87 . depth=108;5'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=RPL23A_20_869(uc010lrb.1)[-] GT:GQ:GD 1/1:95:31 1/1:89:30 1/1:100:47

	Output log file headlines:		Output log file headlines:

	##chr pos ref alt ucsc_name genestrend genestart geneend ref_codon ref_AA alt_codon alt_AA codon_start codon_end genesymbol codonCount type		##chr pos ref alt ucsc_name genestrend genestart geneend ref_codon ref_AA alt_codon alt_AA codon_start codon_end genesymbol codonCount type

Liyanmin at 06:03, 13 December 2010

2010-12-13T06:03:27Z

← Older revision		Revision as of 02:03, 13 December 2010
Line 50:		Line 50:
	Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file		Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file

	1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 10 fields are required and must be of the same order as shown below:		1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 11 fields are required and must be of the same order as shown below:
	string name; "Name of gene"		string name; "Name of gene"
	string chrom; "Chromosome name"		string chrom; "Chromosome name"
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	uint[exonCount] exonStarts; "Exon start positions"		uint[exonCount] exonStarts; "Exon start positions"
	uint[exonCount] exonEnds; "Exon end positions"		uint[exonCount] exonEnds; "Exon end positions"
			string symbol; "Standard gene symbol"
			Note:
	2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other		2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other
	reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is		reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is