annotate test-results/Additional_Details.tsv @ 0:83181dabeb90 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3

#Variant Additional Details Report
#2018-05-18 15:15:25.120629
#CRAVAT version: hybrid
#Analysis done at http://www.cravat.us.
#Job Id: znylund_20180518_111521
#Input file: _VCF_BEDintersect_on_data_65_and_data_6_.vcf
#This report shows analysis results at variant level.
#hg38 genomic.
#N/A
#For more information on CRAVAT, visit http://www.cravat.us.

Input line	ID	Chromosome	Position	Strand	Reference base(s)	Alternate base(s)	Sample ID	HUGO symbol	Sequence ontology	S.O. transcript	S.O. transcript strand	Protein sequence change	S.O. all transcripts	CGC driver class	CGC inheritance	CGC tumor types somatic	CGC tumor types germline	ClinVar disease identifier	ClinVar XRef	COSMIC transcript	COSMIC protein change	COSMIC variant count	ESP6500 AF (European American)	ESP6500 AF (African American)	HGVS Genomic	HGVS Protein	HGVS Protein All	NCI pathway hits	NCI pathway IDs	NCI pathway names	VEST score transcript	VEST p-value	VEST score (missense)	VEST score (frameshift indels)	VEST score (inframe indels)	VEST score (stop-gain)	VEST score (stop-loss)	VEST score (splice site)	All transcripts VEST results
1	VAR516_unknown	chr1	156705422	+	T	C	unknown	CRABP2	MS	ENST00000368221.1	-	K9E	*ENST00000368221.1:K9E(MS),ENST00000621784.4:K9E(MS),ENST00000368222.7:K9E(MS)							ENST00000368221	p.K9E (large_intestine 1)	1	0	0	NC_000001.10:g.156705422T>C	ENST00000368221.1:p.Lys9Glu	*ENST00000368221.1:p.Lys9Glu,ENST00000621784.4:p.Lys9Glu,ENST00000368222.7:p.Lys9Glu	0			ENST00000368221.1:K9E	0.53061	0.2						*ENST00000368221.1:K9E(0.2:0.53061),ENST00000368222.7:K9E(0.187:0.5543),ENST00000621784.4:K9E(0.186:0.55652)
2	VAR517_unknown	chr12	6561055	+	T	C	unknown	NOP2	MS	ENST00000616948.4	-	N408S	ENST00000617555.4:N404S(MS),ENST00000545200.5:N404S(MS),ENST00000541778.5:N404S(MS),ENST00000399466.6:N404S(MS),ENST00000322166.9:N408S(MS),ENST00000537442.5:N408S(MS),ENST00000382421.7:N441S(MS),ENST00000620535.4:N441S(MS),*ENST00000616948.4:N408S(MS)										0	0	NC_000012.10:g.6561055T>C	ENST00000616948.4:p.Asn408Ser	ENST00000617555.4:p.Asn404Ser,ENST00000545200.5:p.Asn404Ser,ENST00000541778.5:p.Asn404Ser,ENST00000399466.6:p.Asn404Ser,ENST00000322166.9:p.Asn408Ser,ENST00000537442.5:p.Asn408Ser,ENST00000382421.7:p.Asn441Ser,ENST00000620535.4:p.Asn441Ser,*ENST00000616948.4:p.Asn408Ser	0			ENST00000616948.4:N408S	0.00324	0.958						ENST00000617555.4:N404S(0.954:0.00354),*ENST00000616948.4:N408S(0.958:0.00324),ENST00000541778.5:N404S(0.869:0.01488),ENST00000537442.5:N408S(0.956:0.00344),ENST00000399466.6:N404S(0.951:0.00374),ENST00000545200.5:N404S(0.953:0.00354),ENST00000620535.4:N441S(0.938:0.00536),ENST00000382421.7:N441S(0.938:0.00536),ENST00000322166.9:N408S(0.954:0.00354)
3	VAR518_unknown	chr12	110339630	+	C	T	unknown	ATP2A2	MS	ENST00000539276.6	+	T557I	ENST00000308664.10:T557I(MS),*ENST00000539276.6:T557I(MS)										0	0	NC_000012.10:g.110339630C>T	ENST00000539276.6:p.Thr557Ile	ENST00000308664.10:p.Thr557Ile,*ENST00000539276.6:p.Thr557Ile	0			ENST00000539276.6:T557I	0.00374	0.951						ENST00000308664.10:T557I(0.822:0.02459),*ENST00000539276.6:T557I(0.951:0.00374)
4	VAR520_unknown	chr14	102011985	+	A	T	unknown	DYNC1H1	MS	ENST00000360184.8	+	R2243S	*ENST00000360184.8:R2243S(MS)							ENST00000360184	p.R2243S (large_intestine 1)	1	0	0	NC_000014.10:g.102011985A>T	ENST00000360184.8:p.Arg2243Ser	*ENST00000360184.8:p.Arg2243Ser	1	94da5dd8-5521-11e7-8f50-0ac135e8bacf	Lissencephaly gene (LIS1) in neuronal migration and development	ENST00000360184.8:R2243S	0.02307	0.829						*ENST00000360184.8:R2243S(0.829:0.02307)
5	VAR521_unknown	chr14	102083954	+	C	T	unknown	HSP90AA1	MS	ENST00000334701.11	-	D515N	ENST00000216281.12:D393N(MS),*ENST00000334701.11:D515N(MS)		somatic	NHL				ENST00000334701	p.D515N (large_intestine 1)	1	0	0	NC_000014.10:g.102083954C>T	ENST00000334701.11:p.Asp515Asn	ENST00000216281.12:p.Asp393Asn,*ENST00000334701.11:p.Asp515Asn	15	3814fa62-5521-11e7-8f50-0ac135e8bacf,32ff1916-5521-11e7-8f50-0ac135e8bacf,a8411a5c-5521-11e7-8f50-0ac135e8bacf,541d7e20-5521-11e7-8f50-0ac135e8bacf,98ad85f0-5521-11e7-8f50-0ac135e8bacf,9697501e-5521-11e7-8f50-0ac135e8bacf,e6f69242-5521-11e7-8f50-0ac135e8bacf,603902ca-5521-11e7-8f50-0ac135e8bacf,bb3d7c4a-5521-11e7-8f50-0ac135e8bacf,b1ac7318-5521-11e7-8f50-0ac135e8bacf,cb348d72-5521-11e7-8f50-0ac135e8bacf,945aa686-5521-11e7-8f50-0ac135e8bacf,4c90f780-5521-11e7-8f50-0ac135e8bacf,e4e93610-5521-11e7-8f50-0ac135e8bacf,6f7a316e-5521-11e7-8f50-0ac135e8bacf	Validated targets of C-MYC transcriptional activation@VEGFR1 specific signals@IL2 signaling events mediated by PI3K@Signaling events mediated by HDAC Class II@Integrin-linked kinase signaling@Integrins in angiogenesis@Class I PI3K signaling events mediated by Akt@Regulation of Telomerase@Glucocorticoid receptor regulatory network@Hypoxic and oxygen homeostasis regulation of HIF-1-alpha@ErbB receptor signaling network@LKB1 signaling events@Signaling events mediated by VEGFR1 and VEGFR2@Class I PI3K signaling events@Regulation of Androgen receptor activity	ENST00000216281.12:D393N	0.02014	0.84						ENST00000334701.11:D515N(0.749:0.04989),*ENST00000216281.12:D393N(0.84:0.02014)
6	VAR522_unknown	chr17	82082606	+	C	T	unknown	FASN	MS	ENST00000306749.3	-	S1947N	ENST00000634990.1:S1945N(MS),*ENST00000306749.3:S1947N(MS)							ENST00000306749	p.S1947N (large_intestine 1)	1	0	0	NC_000017.10:g.82082606C>T	ENST00000306749.3:p.Ser1947Asn	ENST00000634990.1:p.Ser1945Asn,*ENST00000306749.3:p.Ser1947Asn	2	34a994cc-5521-11e7-8f50-0ac135e8bacf,812903c2-5521-11e7-8f50-0ac135e8bacf	Validated transcriptional targets of deltaNp63 isoforms@p73 transcription factor network	ENST00000634990.1:S1945N	0.18611	0.501						ENST00000306749.3:S1947N(0.493:0.19016),*ENST00000634990.1:S1945N(0.501:0.18611)
7	VAR523_unknown	chr19	17205335	+	A	T	unknown	MYO9B	MS	ENST00000594824.5	+	K1688M	ENST00000397274.6:K1688M(MS),ENST00000595618.5:K1688M(MS),*ENST00000594824.5:K1688M(MS)										0	0	NC_000019.10:g.17205335A>T	ENST00000594824.5:p.Lys1688Met	ENST00000397274.6:p.Lys1688Met,ENST00000595618.5:p.Lys1688Met,*ENST00000594824.5:p.Lys1688Met	1	60f3521c-5521-11e7-8f50-0ac135e8bacf	Regulation of RhoA activity	ENST00000397274.6:K1688M	0.20028	0.473						ENST00000594824.5:K1688M(0.464:0.20464),*ENST00000397274.6:K1688M(0.473:0.20028),ENST00000595618.5:K1688M(0.469:0.20231)
9	VAR525_unknown	chr19	17205973	+	T	C	unknown	MYO9B	MS	ENST00000594824.5	+	V1693A	ENST00000397274.6:V1693A(MS),ENST00000595618.5:V1693A(MS),*ENST00000594824.5:V1693A(MS)							ENST00000319396	p.V1693A (thyroid 2)	2	0.399857	0.645631	NC_000019.10:g.17205973T>C	ENST00000594824.5:p.Val1693Ala	ENST00000397274.6:p.Val1693Ala,ENST00000595618.5:p.Val1693Ala,*ENST00000594824.5:p.Val1693Ala	1	60f3521c-5521-11e7-8f50-0ac135e8bacf	Regulation of RhoA activity	ENST00000397274.6:V1693A	0.95254	0.045						ENST00000594824.5:V1693A(0.025:0.98158),*ENST00000397274.6:V1693A(0.045:0.95254),ENST00000595618.5:V1693A(0.042:0.95749)
10	VAR526_unknown	chr19	18856059	+	C	T	unknown	UPF1	MS	ENST00000599848.5	+	A571V	ENST00000262803.9:A560V(MS),*ENST00000599848.5:A571V(MS)							ENST00000262803	p.A560V (large_intestine 1)	1	0	0	NC_000019.10:g.18856059C>T	ENST00000599848.5:p.Ala571Val	ENST00000262803.9:p.Ala560Val,*ENST00000599848.5:p.Ala571Val	0			ENST00000262803.9:A560V	0.09372	0.662						ENST00000599848.5:A571V(0.643:0.10292),*ENST00000262803.9:A560V(0.662:0.09372)