Ensembl - Revision history

Rf at 12:54, 12 May 2016

2016-05-12T12:54:19Z

Rf at 12:51, 12 May 2016

2016-05-12T12:51:43Z

Rf: /* Variant Effect Predictor */

2016-05-12T12:47:31Z

‎Variant Effect Predictor

Rf: /* Variant Effect Predictor */

2016-05-12T12:33:27Z

‎Variant Effect Predictor

Rf at 16:07, 11 May 2016

2016-05-11T16:07:13Z

Rf at 14:23, 11 May 2016

2016-05-11T14:23:21Z

Rf at 14:00, 11 May 2016

2016-05-11T14:00:04Z

Rf at 13:42, 11 May 2016

2016-05-11T13:42:18Z

Rf at 13:39, 11 May 2016

2016-05-11T13:39:53Z

Rf at 13:39, 11 May 2016

2016-05-11T13:39:36Z

← Older revision		Revision as of 12:54, 12 May 2016
Line 46:		Line 46:


−	The program also serves as a "workspace organizer", as one of its aims is to enable a cache (a local storage) of species data in order to circumvent having to download or access remote databases. The options '''--cache''' and '''-offline''' are used for this.	+	The program also serves as a "workspace organizer", as one of its aims is to enable a cache (a local storage) of species data in order to circumvent having to download or access remote databases. The options '''--cache''' and '''--offline''' are used for this.

	The "module load ensembl" command is required to load this software, as it is part of Ensembl's software and also uses Ensembl's Perl API.		The "module load ensembl" command is required to load this software, as it is part of Ensembl's software and also uses Ensembl's Perl API.

@@ Line 42: / Line 42: @@
 = Variant Effect Predictor =
-The "module load ensembl" command is required to load this software, as it is part of enesembl's software and also uses Ensembl's Perl API.
+Examples and use-case (note single dashes mentioned here may need to be double dashes).
 == Example ==

@@ Line 48: / Line 48: @@
 == Example ==
-We have three vaiant on human chromosome 7, we put them in a file like so
+If we take lead from [http://bioinformatics.knowledgeblog.org/2011/06/21/determining-the-effect-of-genomic-variants-using-the-ensembl-variant-effect-predictor/ this] tutorial, we have three variants on human chromosome 7, we put them in a file like so
 117171039 117171039 G/A +

← Older revision		Revision as of 12:33, 12 May 2016
Line 43:		Line 43:

	Essentially this is a workspace organizer, as one of its chief aims is to enable a cache (a local storage) of species data in order to circumvent having to download or access remote databases.		Essentially this is a workspace organizer, as one of its chief aims is to enable a cache (a local storage) of species data in order to circumvent having to download or access remote databases.
		+
		+	The "module load ensembl" command is required to load this software, as it is part of enesembl's software and also uses Ensembl's Perl API.
		+
		+	== Example ==
		+
		+	We have three vaiant on human chromosome 7, we put them in a file like so
		+
		+	7 117171039 117171039 G/A +
		+	7 117171092 117171092 T/C +
		+	7 117171122 117171122 T/C +
		+
		+	On the cluster the cache is set up in '''/shelf/vepcache''' and we include various options, including merged which will search against normals transcripts and RefSeq together:
		+
		+	variant_effect_predictor.pl --cache --dir /shelf/vepcache --offline --species homo_sapiens --merged -i <our_variant_file> -o <our_chosen_outout_filename>
		+
		+	After a successful run, the output is as follows:
		+
		+	## ENSEMBL VARIANT EFFECT PREDICTOR v84
		+	## Output produced at 2016-05-12 13:24:13
		+	## Using cache in /shelf/vepcache/homo_sapiens_merged/84_GRCh37
		+	## Using API version 84, DB version ?
		+	## HGMD-PUBLIC version 20152
		+	## genebuild version 2011-04
		+	## polyphen version 2.2.2
		+	## sift version sift5.2.2
		+	## regbuild version 13
		+	## ESP version 20141103
		+	## ClinVar version 201507
		+	## assembly version GRCh37.p13
		+	## dbSNP version 144
		+	## COSMIC version 71
		+	## gencode version GENCODE 19
		+	## Extra column keys:
		+	## IMPACT : Subjective impact classification of consequence type
		+	## DISTANCE : Shortest distance from variant to transcript
		+	## STRAND : Strand of the feature (1/-1)
		+	## FLAGS : Transcript quality flags
		+	## REFSEQ_MATCH : RefSeq transcript match status
		+	#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra
		+	7_117171039_G/A 7:117171039 A ENSG00000001626 ENST00000454343 Transcript synonymous_variant 492 360 120 A gcG/gcA - IMPACT=LOW;SOURCE=Ensembl;STRAND=1
		+	7_117171039_G/A 7:117171039 A 1080 NM_000492.3 Transcript synonymous_variant 492 360 120 A gcG/gcA - IMPACT=LOW;SOURCE=RefSeq;STRAND=1
		+	7_117171039_G/A 7:117171039 A ENSG00000001626 ENST00000426809 Transcript synonymous_variant 360 360 120 A gcG/gcA - IMPACT=LOW;SOURCE=Ensembl;STRAND=1;FLAGS=cds_end_NF
		+	7_117171039_G/A 7:117171039 A ENSG00000001626 ENST00000446805 Transcript downstream_gene_variant - - - - - - SOURCE=Ensembl;IMPACT=MODIFIER;DISTANCE=7;STRAND=1;FLAGS=cds_end_NF
		+	7_117171039_G/A 7:117171039 A ENSG00000001626 ENST00000003084 Transcript synonymous_variant 492 360 120 A gcG/gcA - IMPACT=LOW;SOURCE=Ensembl;STRAND=1
		+	7_117171092_T/C 7:117171092 C ENSG00000001626 ENST00000454343 Transcript missense_variant 545 413 138 L/P cTa/cCa - SOURCE=Ensembl;IMPACT=MODERATE;STRAND=1
		+	7_117171092_T/C 7:117171092 C 1080 NM_000492.3 Transcript missense_variant 545 413 138 L/P cTa/cCa - IMPACT=MODERATE;SOURCE=RefSeq;STRAND=1
		+	7_117171092_T/C 7:117171092 C ENSG00000001626 ENST00000446805 Transcript downstream_gene_variant - - - - - - SOURCE=Ensembl;IMPACT=MODIFIER;DISTANCE=60;STRAND=1;FLAGS=cds_end_NF
		+	7_117171092_T/C 7:117171092 C ENSG00000001626 ENST00000003084 Transcript missense_variant 545 413 138 L/P cTa/cCa - IMPACT=MODERATE;SOURCE=Ensembl;STRAND=1
		+	7_117171092_T/C 7:117171092 C ENSG00000001626 ENST00000426809 Transcript missense_variant 413 413 138 L/P cTa/cCa - SOURCE=Ensembl;IMPACT=MODERATE;STRAND=1;FLAGS=cds_end_NF
		+	7_117171122_T/C 7:117171122 C ENSG00000001626 ENST00000426809 Transcript missense_variant 443 443 148 I/T aTt/aCt - IMPACT=MODERATE;SOURCE=Ensembl;STRAND=1;FLAGS=cds_end_NF
		+	7_117171122_T/C 7:117171122 C ENSG00000001626 ENST00000003084 Transcript missense_variant 575 443 148 I/T aTt/aCt - IMPACT=MODERATE;SOURCE=Ensembl;STRAND=1
		+	7_117171122_T/C 7:117171122 C ENSG00000001626 ENST00000446805 Transcript downstream_gene_variant - - - - - - SOURCE=Ensembl;IMPACT=MODIFIER;DISTANCE=90;STRAND=1;FLAGS=cds_end_NF
		+	7_117171122_T/C 7:117171122 C 1080 NM_000492.3 Transcript missense_variant 575 443 148 I/T aTt/aCt - SOURCE=RefSeq;IMPACT=MODERATE;STRAND=1
		+	7_117171122_T/C 7:117171122 C ENSG00000001626 ENST00000454343 Transcript missense_variant 575 443 148 I/T aTt/aCt - SOURCE=Ensembl;IMPACT=MODERATE;STRAND=1

← Older revision		Revision as of 16:07, 11 May 2016
Line 39:		Line 39:
	* region_reporter		* region_reporter
	* variant_effect_predictor		* variant_effect_predictor
		+
		+	= Variant Effect Predictor =
		+
		+	Essentially this is a workspace organizer, as one of its chief aims is to enable a cache (a local storage) of species data in order to circumvent having to download or access remote databases.

@@ Line 26: / Line 26: @@
 == ensembl ==
-This poorly named componenet can be referred to as core.
+This poorly named component can be referred to as core.
 ==ensembl-tools ==
-Unlike the other components, this does not contain a modules subdirectory. However, all its compoenents are hidden inside a scripts subdirectory.
+Unlike the other components, this does not contain a modules subdirectory. However, all its components are hidden inside a scripts subdirectory.
 This component contains:

← Older revision		Revision as of 13:42, 11 May 2016
Line 29:		Line 29:

	==ensembl-tools ==		==ensembl-tools ==
		+
		+	Unlike the other components, this does not contain a modules subdirectory

	This component contains:		This component contains:

← Older revision		Revision as of 13:39, 11 May 2016
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	* region_reporter		* region_reporter
	* variant_effect_predictor		* variant_effect_predictor
−
−	~~== em~~

← Older revision		Revision as of 13:39, 11 May 2016
Line 21:		Line 21:
	* ensembl-io		* ensembl-io
	* ensembl-variation		* ensembl-variation
		+
		+	The '''ensembl-tools''' is not retrieved.
		+
		+	== ensembl ==
		+
		+	This poorly named componenet can be referred to as core.
		+
		+	==ensembl-tools ==
		+
		+	This component contains:
		+	* assembly-converter
		+	* id_history_converter
		+	* region_reporter
		+	* variant_effect_predictor
		+
		+	== em