VAT - Revision history

Lukas.habegger: /* gencode2interval */

2011-06-16T14:23:34Z

gencode2interval

← Older revision		Revision as of 14:23, 16 June 2011
Line 279:		Line 279:

	awk '/\t(HAVANA\|ENSEMBL)\tCDS\t/ {print}' gencode.v3c.annotation.GRCh37.gtf \| grep 'gene_type "protein_coding"' \| grep 'transcript_type "protein_coding"' > gencode.v3c.annotation.GRCh37.cds.gtpc.ttpc.gtf		awk '/\t(HAVANA\|ENSEMBL)\tCDS\t/ {print}' gencode.v3c.annotation.GRCh37.gtf \| grep 'gene_type "protein_coding"' \| grep 'transcript_type "protein_coding"' > gencode.v3c.annotation.GRCh37.cds.gtpc.ttpc.gtf
	gencode2interval < ~~encode~~.v3c.annotation.GRCh37.cds.gtpc.ttpc.gtf > ~~encode~~.v3c.annotation.GRCh37.cds.gtpc.ttpc.interval		gencode2interval < gencode.v3c.annotation.GRCh37.cds.gtpc.ttpc.gtf > gencode.v3c.annotation.GRCh37.cds.gtpc.ttpc.interval

	<br>		<br>

Lukas.habegger: /* Setting up the web server */

2011-06-14T18:23:54Z

Setting up the web server

← Older revision		Revision as of 18:23, 14 June 2011
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	$ tar -xvf ALL.2of4intersection.20100804.chr22.tar		$ tar -xvf ALL.2of4intersection.20100804.chr22.tar

	'''View the results''': [http://dynamic.gersteinlab.org/people/lh372~~/dev~~/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804.chr22&annotationSet=gencode3c&type=coding Link to web server]		'''View the results''': [http://dynamic.gersteinlab.org/people/lh372/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804.chr22&annotationSet=gencode3c&type=coding Link to web server]

Lukas.habegger: /* Setting up the web server */

2011-06-13T14:35:46Z

Setting up the web server

← Older revision		Revision as of 14:35, 13 June 2011
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	$ tar -xvf ALL.2of4intersection.20100804.chr22.tar		$ tar -xvf ALL.2of4intersection.20100804.chr22.tar

	'''View the results''': [http://dynamic.gersteinlab.org/people/lh372/dev/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804.chr22&annotationSet=gencode3c Link to web server]		'''View the results''': [http://dynamic.gersteinlab.org/people/lh372/dev/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804.chr22&annotationSet=gencode3c&type=coding Link to web server]

Lukas.habegger at 14:24, 7 June 2011

2011-06-07T14:24:35Z

← Older revision		Revision as of 14:24, 7 June 2011
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	=== VCF ===		=== VCF ===

	The Variant Call Format (VCF) is a tab-delimited text file format to represent a number of different genetic variants including single nucleotide polymorphisms (SNPs), small insertions and deletions (~~Indels~~), and structural variants (SVs). This format was developed as part of the [http://www.1000genomes.org 1000 Genomes Project]. A detailed summary of this file format can be found [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40 here]. The annotation information is captured as part of the '''INFO field''' using the '''VA (Variant Annotation) tag'''. The string with the variant information has the following format:		The Variant Call Format (VCF) is a tab-delimited text file format to represent a number of different genetic variants including single nucleotide polymorphisms (SNPs), small insertions and deletions (indels), and structural variants (SVs). This format was developed as part of the [http://www.1000genomes.org 1000 Genomes Project]. A detailed summary of this file format can be found [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40 here]. The annotation information is captured as part of the '''INFO field''' using the '''VA (Variant Annotation) tag'''. The string with the variant information has the following format:

	'''AlleleNumber:GeneName:GeneId:Strand:Type:FractionOfTranscriptsAffected:{List of transcripts}'''		'''AlleleNumber:GeneName:GeneId:Strand:Type:FractionOfTranscriptsAffected:{List of transcripts}'''

	All annotated variant use the above format to capture information about the gene. The format describing the list of affected transcripts depends on the variant class (SNP, ~~Indel~~, or SV) and the variant type as shown in the table below:		All annotated variant use the above format to capture information about the gene. The format describing the list of affected transcripts depends on the variant class (SNP, indel, or SV) and the variant type as shown in the table below:

	[[File:VariantFormat.png\|1000px]]		[[File:VariantFormat.png\|1000px]]

	The allele number refers to the numbering of the alleles. By definition, the reference allele has zero as the allele number, whereas the alternate alleles are numbered starting at one (some variants have more than one alternate alleles). The type refers to the type of variant. For SNPs, the types can take on the following values (generated by [[#snpMapper\|snpMapper]]): synonymous, nonsynonymous, prematureStop, removedStop, and spliceOverlap. For ~~Indels~~ (generated by [[#indelMapper\|indelMapper]]), the types can take on the following values: spliceOverlap, startOverlap, endOverlap, insertionFS, insertionNFS, deletionFS, deletionNFS, where FS denotes 'frameshift' and NFS indicates 'non-frameshift'. The term spliceOverlap (for both SNPs and ~~Indels~~) refers to a genetic variant that overlaps with a splice site (either two nucleotides downstream of an exon or two nucleotides upstream of an exon).		The allele number refers to the numbering of the alleles. By definition, the reference allele has zero as the allele number, whereas the alternate alleles are numbered starting at one (some variants have more than one alternate alleles). The type refers to the type of variant. For SNPs, the types can take on the following values (generated by [[#snpMapper\|snpMapper]]): synonymous, nonsynonymous, prematureStop, removedStop, and spliceOverlap. For indels (generated by [[#indelMapper\|indelMapper]]), the types can take on the following values: spliceOverlap, startOverlap, endOverlap, insertionFS, insertionNFS, deletionFS, deletionNFS, where FS denotes 'frameshift' and NFS indicates 'non-frameshift'. The term spliceOverlap (for both SNPs and indels) refers to a genetic variant that overlaps with a splice site (either two nucleotides downstream of an exon or two nucleotides upstream of an exon).


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	'''Example 4''': An ~~Indel~~ with two alternate alleles. Each alternate allele leads to a non-frameshift deletion.		'''Example 4''': An indel with two alternate alleles. Each alternate allele leads to a non-frameshift deletion.

	chr7 140118541 . TACAACAACA T,TACA . PASS HP=1;'''VA=1:AC006344.1:ENSG00000236914:+:deletionNFS:1/1:AC006344.1-201:ENST00000434223:66_23_8_LQQQ->L,2:AC006344.1:ENSG00000236914:+:deletionNFS:1/1:AC006344.1-201:ENST00000434223:66_23_8_LQQ->L'''		chr7 140118541 . TACAACAACA T,TACA . PASS HP=1;'''VA=1:AC006344.1:ENSG00000236914:+:deletionNFS:1/1:AC006344.1-201:ENST00000434223:66_23_8_LQQQ->L,2:AC006344.1:ENSG00000236914:+:deletionNFS:1/1:AC006344.1-201:ENST00000434223:66_23_8_LQQ->L'''
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	==== indelMapper ====		==== indelMapper ====

	indelMapper is a program to annotate a set of ~~Indels~~ in [[#VCF\|VCF]] format. The program determines the effect of an ~~Indel~~ on the coding potential (frameshift insertion, non-frameshift insertion, frameshift deletion, non-frameshift deletion, spliceOverlap, startOverlap, endOverlap) of each transcript of a gene.		indelMapper is a program to annotate a set of indels in [[#VCF\|VCF]] format. The program determines the effect of an indel on the coding potential (frameshift insertion, non-frameshift insertion, frameshift deletion, non-frameshift deletion, spliceOverlap, startOverlap, endOverlap) of each transcript of a gene.

	'''Usage''':		'''Usage''':
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	* Inputs: Takes a [[#VCF\|VCF]] input from STDIN		* Inputs: Takes a [[#VCF\|VCF]] input from STDIN
	* Outputs: Outputs annotated ~~Indels~~ in [[#VCF\|VCF]] format. The annotation information is captured as part of the INFO field. For details refer to the [[#VCF\|VCF]] format specification.		* Outputs: Outputs annotated indels in [[#VCF\|VCF]] format. The annotation information is captured as part of the INFO field. For details refer to the [[#VCF\|VCF]] format specification.
	* ''Required arguments''		* ''Required arguments''
	** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.		** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.
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	* Outputs: Generates two output files. The first file, named ''file.geneSummary.txt'', contains the number of variants categorized by type for each gene. A second file, named ''file.sampleSummary.txt'', summarizes number of variants categorized by type for each sample.		* Outputs: Generates two output files. The first file, named ''file.geneSummary.txt'', contains the number of variants categorized by type for each gene. A second file, named ''file.sampleSummary.txt'', summarizes number of variants categorized by type for each sample.
	* ''Required arguments''		* ''Required arguments''
	** file.vcf.gz - VCF file with annotated variants (this can be a mixture of ~~Indels~~ and SNPs). This file must be compressed using [[#bgzip/tabix\|bgzip]] and indexed using the [[#bgzip/tabix\|tabix]] program.		** file.vcf.gz - VCF file with annotated variants (this can be a mixture of indels and SNPs). This file must be compressed using [[#bgzip/tabix\|bgzip]] and indexed using the [[#bgzip/tabix\|tabix]] program.
	** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.		** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.
	* ''Optional arguments''		* ''Optional arguments''
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	* Outputs: Generates an image in PNG format for each gene that has at least one annotated variant.		* Outputs: Generates an image in PNG format for each gene that has at least one annotated variant.
	* ''Required arguments''		* ''Required arguments''
	** file.vcf.gz - VCF file with annotated variants (this can be a mixture of SNPs, ~~Indels~~, and SVs). This file must be compressed using [[#bgzip/tabix\|bgzip]] and indexed using the [[#bgzip/tabix\|tabix]] program.		** file.vcf.gz - VCF file with annotated variants (this can be a mixture of SNPs, indels, and SVs). This file must be compressed using [[#bgzip/tabix\|bgzip]] and indexed using the [[#bgzip/tabix\|tabix]] program.
	** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.		** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.
	** outputDir - The output directory where the images are stored		** outputDir - The output directory where the images are stored
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	* Outputs: Generates a [[#VCF\|VCF]] file for each gene that has at least one annotated variant.		* Outputs: Generates a [[#VCF\|VCF]] file for each gene that has at least one annotated variant.
	* ''Required arguments''		* ''Required arguments''
	** file.vcf.gz - VCF file with annotated variants (this can be a mixture of ~~Indels~~ and SNPs). This file must be compressed using [[#bgzip/tabix\|bgzip]] and indexed using the [[#bgzip/tabix\|tabix]] program.		** file.vcf.gz - VCF file with annotated variants (this can be a mixture of indels and SNPs). This file must be compressed using [[#bgzip/tabix\|bgzip]] and indexed using the [[#bgzip/tabix\|tabix]] program.
	** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.		** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.
	** outputDir - The output directory where [[#VCF\|VCF]] files are stored		** outputDir - The output directory where [[#VCF\|VCF]] files are stored

Lukas.habegger: /* Setting up the web server */

2011-06-06T16:08:21Z

Setting up the web server

← Older revision		Revision as of 16:08, 6 June 2011
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	ALL.2of4intersection.20100804.chr22.vcf.gz.tbi		ALL.2of4intersection.20100804.chr22.vcf.gz.tbi

	Copy the relevant files to the web server ( '''WEB_DATA_DIR''' specified in the [http://info.gersteinlab.org/VAT/download#Installation_and_Configuration_of_VAT VAT configuration file])		Copy the relevant files to the web server ('''WEB_DATA_DIR''' specified in the [http://info.gersteinlab.org/VAT/download#Installation_and_Configuration_of_VAT VAT configuration file])
	$ scp ALL.2of4intersection.20100804.chr22.tar user@webserver:/path/to/WEB_DATA_DIR		$ scp ALL.2of4intersection.20100804.chr22.tar user@webserver:/path/to/WEB_DATA_DIR

Lukas.habegger: /* VCF */

2011-05-25T16:35:14Z

VCF

← Older revision		Revision as of 16:35, 25 May 2011
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	All annotated variant use the above format to capture information about the gene. The format describing the list of affected transcripts depends on the variant class (SNP, Indel, or SV) and the variant type as shown in the table below:		All annotated variant use the above format to capture information about the gene. The format describing the list of affected transcripts depends on the variant class (SNP, Indel, or SV) and the variant type as shown in the table below:

	[[File:VariantFormat.png\|~~750px~~]]		[[File:VariantFormat.png\|1000px]]

	The allele number refers to the numbering of the alleles. By definition, the reference allele has zero as the allele number, whereas the alternate alleles are numbered starting at one (some variants have more than one alternate alleles). The type refers to the type of variant. For SNPs, the types can take on the following values (generated by [[#snpMapper\|snpMapper]]): synonymous, nonsynonymous, prematureStop, removedStop, and spliceOverlap. For Indels (generated by [[#indelMapper\|indelMapper]]), the types can take on the following values: spliceOverlap, startOverlap, endOverlap, insertionFS, insertionNFS, deletionFS, deletionNFS, where FS denotes 'frameshift' and NFS indicates 'non-frameshift'. The term spliceOverlap (for both SNPs and Indels) refers to a genetic variant that overlaps with a splice site (either two nucleotides downstream of an exon or two nucleotides upstream of an exon).		The allele number refers to the numbering of the alleles. By definition, the reference allele has zero as the allele number, whereas the alternate alleles are numbered starting at one (some variants have more than one alternate alleles). The type refers to the type of variant. For SNPs, the types can take on the following values (generated by [[#snpMapper\|snpMapper]]): synonymous, nonsynonymous, prematureStop, removedStop, and spliceOverlap. For Indels (generated by [[#indelMapper\|indelMapper]]), the types can take on the following values: spliceOverlap, startOverlap, endOverlap, insertionFS, insertionNFS, deletionFS, deletionNFS, where FS denotes 'frameshift' and NFS indicates 'non-frameshift'. The term spliceOverlap (for both SNPs and Indels) refers to a genetic variant that overlaps with a splice site (either two nucleotides downstream of an exon or two nucleotides upstream of an exon).

Lukas.habegger: /* VCF */

2011-05-25T16:34:39Z

VCF

← Older revision		Revision as of 16:34, 25 May 2011
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	The Variant Call Format (VCF) is a tab-delimited text file format to represent a number of different genetic variants including single nucleotide polymorphisms (SNPs), small insertions and deletions (Indels), and structural variants (SVs). This format was developed as part of the [http://www.1000genomes.org 1000 Genomes Project]. A detailed summary of this file format can be found [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40 here]. The annotation information is captured as part of the '''INFO field''' using the '''VA (Variant Annotation) tag'''. The string with the variant information has the following format:		The Variant Call Format (VCF) is a tab-delimited text file format to represent a number of different genetic variants including single nucleotide polymorphisms (SNPs), small insertions and deletions (Indels), and structural variants (SVs). This format was developed as part of the [http://www.1000genomes.org 1000 Genomes Project]. A detailed summary of this file format can be found [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40 here]. The annotation information is captured as part of the '''INFO field''' using the '''VA (Variant Annotation) tag'''. The string with the variant information has the following format:

	AlleleNumber:GeneName:GeneId:Strand:Type:FractionOfTranscriptsAffected:{List of transcripts}~~TranscriptName:TranscriptId:TranscriptLength_RelativePositionOfVariant_RelativePositionOfAminoAcid_Substitution~~		'''AlleleNumber:GeneName:GeneId:Strand:Type:FractionOfTranscriptsAffected:{List of transcripts}'''

	[[File:VariantFormat.png\|~~200px~~]]		All annotated variant use the above format to capture information about the gene. The format describing the list of affected transcripts depends on the variant class (SNP, Indel, or SV) and the variant type as shown in the table below:

			[[File:VariantFormat.png\|750px]]

	The allele number refers to the numbering of the alleles. By definition, the reference allele has zero as the allele number, whereas the alternate alleles are numbered starting at one (some variants have more than one alternate alleles). The type refers to the type of variant. For SNPs, the types can take on the following values (generated by [[#snpMapper\|snpMapper]]): synonymous, nonsynonymous, prematureStop, removedStop, and spliceOverlap. For Indels (generated by [[#indelMapper\|indelMapper]]), the types can take on the following values: spliceOverlap, startOverlap, endOverlap, insertionFS, insertionNFS, deletionFS, deletionNFS, where FS denotes 'frameshift' and NFS indicates 'non-frameshift'. The term spliceOverlap (for both SNPs and Indels) refers to a genetic variant that overlaps with a splice site (either two nucleotides downstream of an exon or two nucleotides upstream of an exon).		The allele number refers to the numbering of the alleles. By definition, the reference allele has zero as the allele number, whereas the alternate alleles are numbered starting at one (some variants have more than one alternate alleles). The type refers to the type of variant. For SNPs, the types can take on the following values (generated by [[#snpMapper\|snpMapper]]): synonymous, nonsynonymous, prematureStop, removedStop, and spliceOverlap. For Indels (generated by [[#indelMapper\|indelMapper]]), the types can take on the following values: spliceOverlap, startOverlap, endOverlap, insertionFS, insertionNFS, deletionFS, deletionNFS, where FS denotes 'frameshift' and NFS indicates 'non-frameshift'. The term spliceOverlap (for both SNPs and Indels) refers to a genetic variant that overlaps with a splice site (either two nucleotides downstream of an exon or two nucleotides upstream of an exon).

Lukas.habegger: /* VCF */

2011-05-25T16:33:09Z

VCF

← Older revision		Revision as of 16:33, 25 May 2011
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	AlleleNumber:GeneName:GeneId:Strand:Type:FractionOfTranscriptsAffected:{List of transcripts}TranscriptName:TranscriptId:TranscriptLength_RelativePositionOfVariant_RelativePositionOfAminoAcid_Substitution		AlleleNumber:GeneName:GeneId:Strand:Type:FractionOfTranscriptsAffected:{List of transcripts}TranscriptName:TranscriptId:TranscriptLength_RelativePositionOfVariant_RelativePositionOfAminoAcid_Substitution

	[[File:VariantFormat.png]]		[[File:VariantFormat.png\|200px]]

	The allele number refers to the numbering of the alleles. By definition, the reference allele has zero as the allele number, whereas the alternate alleles are numbered starting at one (some variants have more than one alternate alleles). The type refers to the type of variant. For SNPs, the types can take on the following values (generated by [[#snpMapper\|snpMapper]]): synonymous, nonsynonymous, prematureStop, removedStop, and spliceOverlap. For Indels (generated by [[#indelMapper\|indelMapper]]), the types can take on the following values: spliceOverlap, startOverlap, endOverlap, insertionFS, insertionNFS, deletionFS, deletionNFS, where FS denotes 'frameshift' and NFS indicates 'non-frameshift'. The term spliceOverlap (for both SNPs and Indels) refers to a genetic variant that overlaps with a splice site (either two nucleotides downstream of an exon or two nucleotides upstream of an exon).		The allele number refers to the numbering of the alleles. By definition, the reference allele has zero as the allele number, whereas the alternate alleles are numbered starting at one (some variants have more than one alternate alleles). The type refers to the type of variant. For SNPs, the types can take on the following values (generated by [[#snpMapper\|snpMapper]]): synonymous, nonsynonymous, prematureStop, removedStop, and spliceOverlap. For Indels (generated by [[#indelMapper\|indelMapper]]), the types can take on the following values: spliceOverlap, startOverlap, endOverlap, insertionFS, insertionNFS, deletionFS, deletionNFS, where FS denotes 'frameshift' and NFS indicates 'non-frameshift'. The term spliceOverlap (for both SNPs and Indels) refers to a genetic variant that overlaps with a splice site (either two nucleotides downstream of an exon or two nucleotides upstream of an exon).

Lukas.habegger: /* VCF */

2011-05-25T16:31:36Z

VCF

← Older revision		Revision as of 16:31, 25 May 2011
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	AlleleNumber:GeneName:GeneId:Strand:Type:FractionOfTranscriptsAffected:{List of transcripts}TranscriptName:TranscriptId:TranscriptLength_RelativePositionOfVariant_RelativePositionOfAminoAcid_Substitution		AlleleNumber:GeneName:GeneId:Strand:Type:FractionOfTranscriptsAffected:{List of transcripts}TranscriptName:TranscriptId:TranscriptLength_RelativePositionOfVariant_RelativePositionOfAminoAcid_Substitution

			[[File:VariantFormat.png]]

	The allele number refers to the numbering of the alleles. By definition, the reference allele has zero as the allele number, whereas the alternate alleles are numbered starting at one (some variants have more than one alternate alleles). The type refers to the type of variant. For SNPs, the types can take on the following values (generated by [[#snpMapper\|snpMapper]]): synonymous, nonsynonymous, prematureStop, removedStop, and spliceOverlap. For Indels (generated by [[#indelMapper\|indelMapper]]), the types can take on the following values: spliceOverlap, startOverlap, endOverlap, insertionFS, insertionNFS, deletionFS, deletionNFS, where FS denotes 'frameshift' and NFS indicates 'non-frameshift'. The term spliceOverlap (for both SNPs and Indels) refers to a genetic variant that overlaps with a splice site (either two nucleotides downstream of an exon or two nucleotides upstream of an exon).		The allele number refers to the numbering of the alleles. By definition, the reference allele has zero as the allele number, whereas the alternate alleles are numbered starting at one (some variants have more than one alternate alleles). The type refers to the type of variant. For SNPs, the types can take on the following values (generated by [[#snpMapper\|snpMapper]]): synonymous, nonsynonymous, prematureStop, removedStop, and spliceOverlap. For Indels (generated by [[#indelMapper\|indelMapper]]), the types can take on the following values: spliceOverlap, startOverlap, endOverlap, insertionFS, insertionNFS, deletionFS, deletionNFS, where FS denotes 'frameshift' and NFS indicates 'non-frameshift'. The term spliceOverlap (for both SNPs and Indels) refers to a genetic variant that overlaps with a splice site (either two nucleotides downstream of an exon or two nucleotides upstream of an exon).

Lukas.habegger: /* vcfSubsetByGene */

2011-05-25T16:24:25Z

vcfSubsetByGene

← Older revision		Revision as of 16:24, 25 May 2011
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	* Outputs: Generates a [[#VCF\|VCF]] file for each gene that has at least one annotated variant.		* Outputs: Generates a [[#VCF\|VCF]] file for each gene that has at least one annotated variant.
	* ''Required arguments''		* ''Required arguments''
	** file.vcf.gz - VCF file with annotated variants (this can be a mixture of ~~indels~~ and SNPs). This file must be compressed using [[#bgzip/tabix\|bgzip]] and indexed using the [[#bgzip/tabix\|tabix]] program.		** file.vcf.gz - VCF file with annotated variants (this can be a mixture of Indels and SNPs). This file must be compressed using [[#bgzip/tabix\|bgzip]] and indexed using the [[#bgzip/tabix\|tabix]] program.
	** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.		** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.
	** outputDir - The output directory where [[#VCF\|VCF]] files are stored		** outputDir - The output directory where [[#VCF\|VCF]] files are stored

← Older revision		Revision as of 16:24, 25 May 2011
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	* Outputs: Generates a [[#VCF\|VCF]] file for each gene that has at least one annotated variant.		* Outputs: Generates a [[#VCF\|VCF]] file for each gene that has at least one annotated variant.
	* ''Required arguments''		* ''Required arguments''
	** file.vcf.gz - VCF file with annotated variants (this can be a mixture of ~~indels~~ and SNPs). This file must be compressed using [[#bgzip/tabix\|bgzip]] and indexed using the [[#bgzip/tabix\|tabix]] program.		** file.vcf.gz - VCF file with annotated variants (this can be a mixture of Indels and SNPs). This file must be compressed using [[#bgzip/tabix\|bgzip]] and indexed using the [[#bgzip/tabix\|tabix]] program.
	** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.		** annotation.interval - Annotation file representing the genomic coordinates of the gene models in [[#Interval\|Interval]] format. Each line in this file represents a transcript. This file is typically generated using the [[#gencode2interval\|gencode2interval]] program.
	** outputDir - The output directory where [[#VCF\|VCF]] files are stored		** outputDir - The output directory where [[#VCF\|VCF]] files are stored