Search and Download

TCGAbiolinks has provided a few functions to download mutation data from GDC. There are two options to download the data:

Use GDCquery_Maf which will download MAF aligned against hg38
Use GDCquery, GDCdownload and GDCpreprare to downoad MAF aligned against hg19

Mutation data (hg38)

This exmaple will download MAF (mutation annotation files) for variant calling pipeline muse. Pipelines options are: muse, varscan2, somaticsniper, mutect. For more information please access GDC docs.

maf <- GDCquery_Maf("CHOL", pipelines = "muse")

# Only first 50 to make render faster
datatable(maf[1:20,],
          filter = 'top',
          options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
          rownames = FALSE)

Show entries

Search:

Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	HGVSc	HGVSp	HGVSp_Short	Transcript_ID	Exon_Number	t_depth	t_ref_count	t_alt_count	n_depth	n_ref_count	n_alt_count	all_effects	Allele	Gene	Feature	Feature_type	One_Consequence	Consequence	cDNA_position	CDS_position	Protein_position	Amino_acids	Codons	Existing_variation	ALLELE_NUM	DISTANCE	TRANSCRIPT_STRAND	SYMBOL	SYMBOL_SOURCE	HGNC_ID	BIOTYPE	CANONICAL	CCDS	ENSP	SWISSPROT	TREMBL	UNIPARC	RefSeq	SIFT	PolyPhen	EXON	INTRON	DOMAINS	GMAF	AFR_MAF	AMR_MAF	ASN_MAF	EAS_MAF	EUR_MAF	SAS_MAF	AA_MAF	EA_MAF	CLIN_SIG	SOMATIC	PUBMED	MOTIF_NAME	MOTIF_POS	HIGH_INF_POS	MOTIF_SCORE_CHANGE	IMPACT	PICK	VARIANT_CLASS	TSL	HGVS_OFFSET	PHENO	MINIMISED	ExAC_AF	ExAC_AF_Adj	ExAC_AF_AFR	ExAC_AF_AMR	ExAC_AF_EAS	ExAC_AF_FIN	ExAC_AF_NFE	ExAC_AF_OTH	ExAC_AF_SAS	GENE_PHENO	FILTER	CONTEXT	src_vcf_id	tumor_bam_uuid	normal_bam_uuid	case_id	GDC_FILTER	COSMIC	MC3_Overlap	GDC_Validation_Status
	752 203102				398326 240211162	398326 240211162																																	15 160	7 94	5 71	13 63																		-1 1																																				1 5				0.000008275 0.000041180	0.000008317 0.000041440	0.000000 0.000195	0.00000000 0.00026140	0.0000000 0.0001157		0.00001503 0.00001515	0.000000 0.001106	0.00000000 0.00006084

Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Mutation_Status	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	HGVSc	HGVSp	HGVSp_Short	Transcript_ID	Exon_Number	t_depth	t_ref_count	t_alt_count	n_depth	all_effects	Allele	Gene	Feature	Feature_type	One_Consequence	Consequence	cDNA_position	CDS_position	Protein_position	Amino_acids	Codons	ALLELE_NUM	TRANSCRIPT_STRAND	SYMBOL	SYMBOL_SOURCE	HGNC_ID	BIOTYPE	CANONICAL	CCDS	ENSP	SWISSPROT	TREMBL	UNIPARC	RefSeq	SIFT	PolyPhen	EXON	DOMAINS	IMPACT	PICK	VARIANT_CLASS	TSL	MINIMISED	FILTER	CONTEXT	src_vcf_id	tumor_bam_uuid	normal_bam_uuid	case_id	COSMIC	MC3_Overlap	GDC_Validation_Status

FMN2	56776	WUGSC	GRCh38	chr1	240211162	240211162	+	Nonsense_Mutation	SNP	T	T	A		TCGA-4G-AAZT-01A-11D-A417-09	TCGA-4G-AAZT-10A-01D-A41A-09	Somatic	Illumina HiSeq 2000	24c3dc90-d1f2-4256-9909-0d0c939c178f	e75e6102-170d-49e4-89e6-7687cad1f6b6	c.3992T>A	p.Leu1331Ter	p.L1331*	ENST00000319653	6/18	58	34	24	26	FMN2,stop_gained,p.L1331*,ENST00000319653,NM_020066.4&NM_001305424.1;FMN2,downstream_gene_variant,,ENST00000447095,	A	ENSG00000155816	ENST00000319653	Transcript	stop_gained	stop_gained	4222/6434	3992/5169	1331/1722	L/*	tTa/tAa	1	1	FMN2	HGNC	HGNC:14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	Q9NZ56			NM_020066.4;NM_001305424.1			6/18	Pfam_domain:PF02181;SMART_domains:SM00498;Superfamily_domains:SSF101447	HIGH	1	SNV	5	1	PASS	GGAATTATTTT	263c128d-cf0a-4a8b-bafa-fa84d9baeb2c	5a30d2bd-9cab-44ef-9071-0b34d386a9c0	2c662e9d-0c78-4ec4-bc57-3f9573ffc678	b10c64c2-7fd2-4210-b975-034affb14b57	COSM4571189	True	Unknown
PAX3	5077	WUGSC	GRCh38	chr2	222297158	222297158	+	Missense_Mutation	SNP	G	G	T	novel	TCGA-4G-AAZT-01A-11D-A417-09	TCGA-4G-AAZT-10A-01D-A41A-09	Somatic	Illumina HiSeq 2000	24c3dc90-d1f2-4256-9909-0d0c939c178f	e75e6102-170d-49e4-89e6-7687cad1f6b6	c.141C>A	p.Asn47Lys	p.N47K	ENST00000350526	2/8	52	19	32	29	PAX3,missense_variant,p.N47K,ENST00000350526,NM_181457.3;PAX3,missense_variant,p.N47K,ENST00000392069,NM_181459.3;PAX3,missense_variant,p.N47K,ENST00000344493,NM_181461.3;PAX3,missense_variant,p.N47K,ENST00000392070,NM_181458.3;PAX3,missense_variant,p.N47K,ENST00000336840,NM_181460.3;PAX3,missense_variant,p.N47K,ENST00000409551,NM_001127366.2;PAX3,missense_variant,p.N47K,ENST00000409828,NM_000438.5;PAX3,missense_variant,p.N47K,ENST00000258387,NM_013942.4;CCDC140,upstream_gene_variant,,ENST00000295226,NM_153038.1	T	ENSG00000135903	ENST00000350526	Transcript	missense_variant	missense_variant	278/3610	141/1440	47/479	N/K	aaC/aaA	1	-1	PAX3	HGNC	HGNC:8617	protein_coding		CCDS42826.1	ENSP00000343052	P23760	A0A024R470	UPI0000131369	NM_181457.3	deleterious(0)	possibly_damaging(0.813)	2/8	Pfam_domain:PF00292;Prints_domain:PR00027;SMART_domains:SM00351;PROSITE_profiles:PS51057;Superfamily_domains:SSF46689	MODERATE		SNV	5	1	PASS	CTGCCGTTGAT	263c128d-cf0a-4a8b-bafa-fa84d9baeb2c	5a30d2bd-9cab-44ef-9071-0b34d386a9c0	2c662e9d-0c78-4ec4-bc57-3f9573ffc678	b10c64c2-7fd2-4210-b975-034affb14b57		True	Unknown
NYAP2	57624	WUGSC	GRCh38	chr2	225582898	225582898	+	Missense_Mutation	SNP	C	C	T	novel	TCGA-4G-AAZT-01A-11D-A417-09	TCGA-4G-AAZT-10A-01D-A41A-09	Somatic	Illumina HiSeq 2000	24c3dc90-d1f2-4256-9909-0d0c939c178f	e75e6102-170d-49e4-89e6-7687cad1f6b6	c.1481C>T	p.Thr494Ile	p.T494I	ENST00000272907	4/6	47	30	17	25	NYAP2,missense_variant,p.T494I,ENST00000272907,NM_020864.1	T	ENSG00000144460	ENST00000272907	Transcript	missense_variant	missense_variant	1894/4828	1481/1962	494/653	T/I	aCc/aTc	1	1	NYAP2	HGNC	HGNC:29291	protein_coding	YES	CCDS46529.1	ENSP00000272907	Q9P242		UPI00001C1DB6	NM_020864.1	deleterious(0.05)	benign(0.407)	4/6		MODERATE	1	SNV	1	1	PASS	GAACACCTACG	263c128d-cf0a-4a8b-bafa-fa84d9baeb2c	5a30d2bd-9cab-44ef-9071-0b34d386a9c0	2c662e9d-0c78-4ec4-bc57-3f9573ffc678	b10c64c2-7fd2-4210-b975-034affb14b57		True	Unknown
CHL1	10752	WUGSC	GRCh38	chr3	398326	398326	+	Missense_Mutation	SNP	C	C	G	novel	TCGA-4G-AAZT-01A-11D-A417-09	TCGA-4G-AAZT-10A-01D-A41A-09	Somatic	Illumina HiSeq 2000	24c3dc90-d1f2-4256-9909-0d0c939c178f	e75e6102-170d-49e4-89e6-7687cad1f6b6	c.3146C>G	p.Thr1049Ser	p.T1049S	ENST00000397491	24/27	57	17	40	39	CHL1,missense_variant,p.T1065S,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.T1049S,ENST00000397491,NM_001253387.1;CHL1,intron_variant,,ENST00000620033,NM_001253388.1;CHL1,intron_variant,,ENST00000445697,;CHL1,3_prime_UTR_variant,,ENST00000453040,	G	ENSG00000134121	ENST00000397491	Transcript	missense_variant	missense_variant	3613/5235	3146/3627	1049/1208	T/S	aCt/aGt	1	1	CHL1	HGNC	HGNC:1939	protein_coding		CCDS58812.1	ENSP00000380628	O00533		UPI0000E08093	NM_001253387.1	tolerated(0.34)	benign(0.271)	24/27		MODERATE		SNV	1	1	PASS	AATGACTAAGA	263c128d-cf0a-4a8b-bafa-fa84d9baeb2c	5a30d2bd-9cab-44ef-9071-0b34d386a9c0	2c662e9d-0c78-4ec4-bc57-3f9573ffc678	b10c64c2-7fd2-4210-b975-034affb14b57		True	Unknown
NUP210	23225	WUGSC	GRCh38	chr3	13341792	13341792	+	Missense_Mutation	SNP	T	T	G	novel	TCGA-4G-AAZT-01A-11D-A417-09	TCGA-4G-AAZT-10A-01D-A41A-09	Somatic	Illumina HiSeq 2000	24c3dc90-d1f2-4256-9909-0d0c939c178f	e75e6102-170d-49e4-89e6-7687cad1f6b6	c.3184A>C	p.Asn1062His	p.N1062H	ENST00000254508	23/40	33	13	20	25	NUP210,missense_variant,p.N1062H,ENST00000254508,NM_024923.3;NUP210,upstream_gene_variant,,ENST00000485755,	G	ENSG00000132182	ENST00000254508	Transcript	missense_variant	missense_variant	3267/7193	3184/5664	1062/1887	N/H	Aat/Cat	1	-1	NUP210	HGNC	HGNC:30052	protein_coding	YES	CCDS33704.1	ENSP00000254508	Q8TEM1		UPI00001600AF	NM_024923.3	deleterious(0)	benign(0)	23/40		MODERATE	1	SNV	2	1	PASS	TTTATTGGTCA	263c128d-cf0a-4a8b-bafa-fa84d9baeb2c	5a30d2bd-9cab-44ef-9071-0b34d386a9c0	2c662e9d-0c78-4ec4-bc57-3f9573ffc678	b10c64c2-7fd2-4210-b975-034affb14b57		True	Unknown

Showing 1 to 5 of 20 entries

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Mutation data (hg19)

This exmaple will download MAF (mutation annotation files) aligned against hg19 (Old TCGA maf files)

query.maf.hg19 <- GDCquery(project = "TCGA-CHOL", 
                           data.category = "Simple nucleotide variation", 
                           data.type = "Simple somatic mutation",
                           access = "open", 
                           legacy = TRUE)

# Check maf availables
datatable(dplyr::select(getResults(query.maf.hg19),-contains("cases")),
          filter = 'top',
          options = list(scrollX = TRUE, keys = TRUE, pageLength = 10), 
          rownames = FALSE)

Show entries

Search:

data_release	data_type	tags	file_name	submitter_id	file_id	file_size	state_comment	id	md5sum	updated_datetime	data_format	access	platform	state	version	data_category	type	experimental_strategy	created_datetime	project	code	center_name	center_short_name	center_center_id	center_namespace	center_center_type	tissue.definition
						785408 4274149

data_type	tags	file_name	file_id	file_size	id	md5sum	updated_datetime	data_format	access	platform	state	data_category	type	experimental_strategy	created_datetime	project	code	center_name	center_short_name	center_center_id	center_namespace	center_center_type	tissue.definition

Simple somatic mutation	snv,somatic	hgsc.bcm.edu_CHOL.IlluminaGA_DNASeq.1.somatic.maf	a8532d87-1eae-4289-8aea-3255d7b313cf	2482745	a8532d87-1eae-4289-8aea-3255d7b313cf	8db4269d8aba6d8d397e2761e24e8e6e	2017-03-05T09:28:11.866514-06:00	MAF	open	Mixed platforms	live	Simple nucleotide variation	file	DNA-Seq		TCGA-CHOL	10	Baylor College of Medicine	BCM	d3b8c887-498b-5490-903e-760403c68307	hgsc.bcm.edu	GSC	Primary solid Tumor
Simple somatic mutation	snv,somatic	bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf	0d2e60c5-dd32-4a19-b600-7e76496f4f94	1012118	0d2e60c5-dd32-4a19-b600-7e76496f4f94	47268aa46006c53013466f740a3e1462	2017-03-05T10:25:29.699247-06:00	MAF	open	Illumina HiSeq	live	Simple nucleotide variation	file	DNA-Seq		TCGA-CHOL	34	Canada's Michael Smith Genome Sciences Centre	BCGSC	380301b3-6f8d-581d-a81f-f4dd462df12b	bcgsc.ca	GSC	Primary solid Tumor
Simple somatic mutation	somatic,snv	ucsc.edu_CHOL.IlluminaGA_DNASeq_automated.Level_2.1.0.0.somatic.maf	e45ec3d9-adcc-43db-a71c-9edaf7d11c86	785408	e45ec3d9-adcc-43db-a71c-9edaf7d11c86	b44be3f2e6a994be766cc881a3143b2b	2017-03-05T18:49:13.665667-06:00	MAF	open	Illumina GA	live	Simple nucleotide variation	file	DNA-Seq		TCGA-CHOL	25	University of California, Santa Cruz	UCSC	79cc1498-5d7f-5eae-b631-e74b78c13581	ucsc.edu	GSC	Primary solid Tumor
Simple somatic mutation	snv,somatic	hgsc.bcm.edu_CHOL.IlluminaGA_DNASeq.1.somatic.maf	448661d5-a89a-480e-adfd-1cce8eb74e70	2052077	448661d5-a89a-480e-adfd-1cce8eb74e70	ee6d4a3810593268b8038dfb13999ddd	2017-03-05T00:22:24.678827-06:00	MAF	open	Illumina GA	live	Simple nucleotide variation	file	DNA-Seq		TCGA-CHOL	10	Baylor College of Medicine	BCM	d3b8c887-498b-5490-903e-760403c68307	hgsc.bcm.edu	GSC	Primary solid Tumor
Simple somatic mutation	snv,somatic	gsc_CHOL_pairs.aggregated.capture.tcga.uuid.automated.somatic.maf	2d9ed46f-36a5-4f87-9304-74ce626ae96d	4274149	2d9ed46f-36a5-4f87-9304-74ce626ae96d	9288f4c155d47f4cc090eee3312e09c2	2017-03-05T12:45:35.461959-06:00	MAF	open	Illumina GA	live	Simple nucleotide variation	file	DNA-Seq	2016-06-13T17:02:09.527369-05:00	TCGA-CHOL	08	Broad Institute of MIT and Harvard	BI	61d634b8-e8dd-58bf-9a65-1233dc7c8c6a	broad.mit.edu	GSC	Primary solid Tumor

Showing 1 to 5 of 5 entries

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query.maf.hg19 <- GDCquery(project = "TCGA-CHOL", 
                           data.category = "Simple nucleotide variation", 
                           data.type = "Simple somatic mutation",
                           access = "open", 
                           file.type = "bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf",
                           legacy = TRUE)
GDCdownload(query.maf.hg19)
maf <- GDCprepare(query.maf.hg19)

# Only first 50 to make render faster
datatable(maf[1:20,],
          filter = 'top',
          options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
          rownames = FALSE)

Show entries

Search:

Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	HGVSc	HGVSp	HGVSp_Short	Transcript_ID	Exon_Number	t_depth	t_ref_count	t_alt_count	n_depth	n_ref_count	n_alt_count	all_effects	Allele	Gene	Feature	Feature_type	One_Consequence	Consequence	cDNA_position	CDS_position	Protein_position	Amino_acids	Codons	Existing_variation	ALLELE_NUM	DISTANCE	TRANSCRIPT_STRAND	SYMBOL	SYMBOL_SOURCE	HGNC_ID	BIOTYPE	CANONICAL	CCDS	ENSP	SWISSPROT	TREMBL	UNIPARC	RefSeq	SIFT	PolyPhen	EXON	INTRON	DOMAINS	GMAF	AFR_MAF	AMR_MAF	ASN_MAF	EAS_MAF	EUR_MAF	SAS_MAF	AA_MAF	EA_MAF	CLIN_SIG	SOMATIC	PUBMED	MOTIF_NAME	MOTIF_POS	HIGH_INF_POS	MOTIF_SCORE_CHANGE	IMPACT	PICK	VARIANT_CLASS	TSL	HGVS_OFFSET	PHENO	MINIMISED	ExAC_AF	ExAC_AF_Adj	ExAC_AF_AFR	ExAC_AF_AMR	ExAC_AF_EAS	ExAC_AF_FIN	ExAC_AF_NFE	ExAC_AF_OTH	ExAC_AF_SAS	GENE_PHENO	FILTER	CONTEXT	src_vcf_id	tumor_bam_uuid	normal_bam_uuid	case_id	GDC_FILTER	COSMIC	MC3_Overlap	GDC_Validation_Status
	752 203102				398326 240211162	398326 240211162																																	15 160	7 94	5 71	13 63																		-1 1																																				1 5				0.000008275 0.000041180	0.000008317 0.000041440	0.000000 0.000195	0.00000000 0.00026140	0.0000000 0.0001157		0.00001503 0.00001515	0.000000 0.001106	0.00000000 0.00006084

Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Mutation_Status	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	HGVSc	HGVSp	HGVSp_Short	Transcript_ID	Exon_Number	t_depth	t_ref_count	t_alt_count	n_depth	all_effects	Allele	Gene	Feature	Feature_type	One_Consequence	Consequence	cDNA_position	CDS_position	Protein_position	Amino_acids	Codons	ALLELE_NUM	TRANSCRIPT_STRAND	SYMBOL	SYMBOL_SOURCE	HGNC_ID	BIOTYPE	CANONICAL	CCDS	ENSP	SWISSPROT	TREMBL	UNIPARC	RefSeq	SIFT	PolyPhen	EXON	DOMAINS	IMPACT	PICK	VARIANT_CLASS	TSL	MINIMISED	FILTER	CONTEXT	src_vcf_id	tumor_bam_uuid	normal_bam_uuid	case_id	COSMIC	MC3_Overlap	GDC_Validation_Status

FMN2	56776	WUGSC	GRCh38	chr1	240211162	240211162	+	Nonsense_Mutation	SNP	T	T	A		TCGA-4G-AAZT-01A-11D-A417-09	TCGA-4G-AAZT-10A-01D-A41A-09	Somatic	Illumina HiSeq 2000	24c3dc90-d1f2-4256-9909-0d0c939c178f	e75e6102-170d-49e4-89e6-7687cad1f6b6	c.3992T>A	p.Leu1331Ter	p.L1331*	ENST00000319653	6/18	58	34	24	26	FMN2,stop_gained,p.L1331*,ENST00000319653,NM_020066.4&NM_001305424.1;FMN2,downstream_gene_variant,,ENST00000447095,	A	ENSG00000155816	ENST00000319653	Transcript	stop_gained	stop_gained	4222/6434	3992/5169	1331/1722	L/*	tTa/tAa	1	1	FMN2	HGNC	HGNC:14074	protein_coding	YES	CCDS31069.2	ENSP00000318884	Q9NZ56			NM_020066.4;NM_001305424.1			6/18	Pfam_domain:PF02181;SMART_domains:SM00498;Superfamily_domains:SSF101447	HIGH	1	SNV	5	1	PASS	GGAATTATTTT	263c128d-cf0a-4a8b-bafa-fa84d9baeb2c	5a30d2bd-9cab-44ef-9071-0b34d386a9c0	2c662e9d-0c78-4ec4-bc57-3f9573ffc678	b10c64c2-7fd2-4210-b975-034affb14b57	COSM4571189	True	Unknown
PAX3	5077	WUGSC	GRCh38	chr2	222297158	222297158	+	Missense_Mutation	SNP	G	G	T	novel	TCGA-4G-AAZT-01A-11D-A417-09	TCGA-4G-AAZT-10A-01D-A41A-09	Somatic	Illumina HiSeq 2000	24c3dc90-d1f2-4256-9909-0d0c939c178f	e75e6102-170d-49e4-89e6-7687cad1f6b6	c.141C>A	p.Asn47Lys	p.N47K	ENST00000350526	2/8	52	19	32	29	PAX3,missense_variant,p.N47K,ENST00000350526,NM_181457.3;PAX3,missense_variant,p.N47K,ENST00000392069,NM_181459.3;PAX3,missense_variant,p.N47K,ENST00000344493,NM_181461.3;PAX3,missense_variant,p.N47K,ENST00000392070,NM_181458.3;PAX3,missense_variant,p.N47K,ENST00000336840,NM_181460.3;PAX3,missense_variant,p.N47K,ENST00000409551,NM_001127366.2;PAX3,missense_variant,p.N47K,ENST00000409828,NM_000438.5;PAX3,missense_variant,p.N47K,ENST00000258387,NM_013942.4;CCDC140,upstream_gene_variant,,ENST00000295226,NM_153038.1	T	ENSG00000135903	ENST00000350526	Transcript	missense_variant	missense_variant	278/3610	141/1440	47/479	N/K	aaC/aaA	1	-1	PAX3	HGNC	HGNC:8617	protein_coding		CCDS42826.1	ENSP00000343052	P23760	A0A024R470	UPI0000131369	NM_181457.3	deleterious(0)	possibly_damaging(0.813)	2/8	Pfam_domain:PF00292;Prints_domain:PR00027;SMART_domains:SM00351;PROSITE_profiles:PS51057;Superfamily_domains:SSF46689	MODERATE		SNV	5	1	PASS	CTGCCGTTGAT	263c128d-cf0a-4a8b-bafa-fa84d9baeb2c	5a30d2bd-9cab-44ef-9071-0b34d386a9c0	2c662e9d-0c78-4ec4-bc57-3f9573ffc678	b10c64c2-7fd2-4210-b975-034affb14b57		True	Unknown
NYAP2	57624	WUGSC	GRCh38	chr2	225582898	225582898	+	Missense_Mutation	SNP	C	C	T	novel	TCGA-4G-AAZT-01A-11D-A417-09	TCGA-4G-AAZT-10A-01D-A41A-09	Somatic	Illumina HiSeq 2000	24c3dc90-d1f2-4256-9909-0d0c939c178f	e75e6102-170d-49e4-89e6-7687cad1f6b6	c.1481C>T	p.Thr494Ile	p.T494I	ENST00000272907	4/6	47	30	17	25	NYAP2,missense_variant,p.T494I,ENST00000272907,NM_020864.1	T	ENSG00000144460	ENST00000272907	Transcript	missense_variant	missense_variant	1894/4828	1481/1962	494/653	T/I	aCc/aTc	1	1	NYAP2	HGNC	HGNC:29291	protein_coding	YES	CCDS46529.1	ENSP00000272907	Q9P242		UPI00001C1DB6	NM_020864.1	deleterious(0.05)	benign(0.407)	4/6		MODERATE	1	SNV	1	1	PASS	GAACACCTACG	263c128d-cf0a-4a8b-bafa-fa84d9baeb2c	5a30d2bd-9cab-44ef-9071-0b34d386a9c0	2c662e9d-0c78-4ec4-bc57-3f9573ffc678	b10c64c2-7fd2-4210-b975-034affb14b57		True	Unknown
CHL1	10752	WUGSC	GRCh38	chr3	398326	398326	+	Missense_Mutation	SNP	C	C	G	novel	TCGA-4G-AAZT-01A-11D-A417-09	TCGA-4G-AAZT-10A-01D-A41A-09	Somatic	Illumina HiSeq 2000	24c3dc90-d1f2-4256-9909-0d0c939c178f	e75e6102-170d-49e4-89e6-7687cad1f6b6	c.3146C>G	p.Thr1049Ser	p.T1049S	ENST00000397491	24/27	57	17	40	39	CHL1,missense_variant,p.T1065S,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.T1049S,ENST00000397491,NM_001253387.1;CHL1,intron_variant,,ENST00000620033,NM_001253388.1;CHL1,intron_variant,,ENST00000445697,;CHL1,3_prime_UTR_variant,,ENST00000453040,	G	ENSG00000134121	ENST00000397491	Transcript	missense_variant	missense_variant	3613/5235	3146/3627	1049/1208	T/S	aCt/aGt	1	1	CHL1	HGNC	HGNC:1939	protein_coding		CCDS58812.1	ENSP00000380628	O00533		UPI0000E08093	NM_001253387.1	tolerated(0.34)	benign(0.271)	24/27		MODERATE		SNV	1	1	PASS	AATGACTAAGA	263c128d-cf0a-4a8b-bafa-fa84d9baeb2c	5a30d2bd-9cab-44ef-9071-0b34d386a9c0	2c662e9d-0c78-4ec4-bc57-3f9573ffc678	b10c64c2-7fd2-4210-b975-034affb14b57		True	Unknown
NUP210	23225	WUGSC	GRCh38	chr3	13341792	13341792	+	Missense_Mutation	SNP	T	T	G	novel	TCGA-4G-AAZT-01A-11D-A417-09	TCGA-4G-AAZT-10A-01D-A41A-09	Somatic	Illumina HiSeq 2000	24c3dc90-d1f2-4256-9909-0d0c939c178f	e75e6102-170d-49e4-89e6-7687cad1f6b6	c.3184A>C	p.Asn1062His	p.N1062H	ENST00000254508	23/40	33	13	20	25	NUP210,missense_variant,p.N1062H,ENST00000254508,NM_024923.3;NUP210,upstream_gene_variant,,ENST00000485755,	G	ENSG00000132182	ENST00000254508	Transcript	missense_variant	missense_variant	3267/7193	3184/5664	1062/1887	N/H	Aat/Cat	1	-1	NUP210	HGNC	HGNC:30052	protein_coding	YES	CCDS33704.1	ENSP00000254508	Q8TEM1		UPI00001600AF	NM_024923.3	deleterious(0)	benign(0)	23/40		MODERATE	1	SNV	2	1	PASS	TTTATTGGTCA	263c128d-cf0a-4a8b-bafa-fa84d9baeb2c	5a30d2bd-9cab-44ef-9071-0b34d386a9c0	2c662e9d-0c78-4ec4-bc57-3f9573ffc678	b10c64c2-7fd2-4210-b975-034affb14b57		True	Unknown

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Visualize the data

To visualize the data you can use the Bioconductor package maftools. For more information, please check its vignette.

library(maftools)
library(dplyr)
maf <- GDCquery_Maf("CHOL", pipelines = "muse") %>% read.maf

datatable(getSampleSummary(maf),
          filter = 'top',
          options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
          rownames = FALSE)
plotmafSummary(maf = maf, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE)

oncoplot(maf = maf, top = 10, removeNonMutated = TRUE)
titv = titv(maf = maf, plot = FALSE, useSyn = TRUE)
#plot titv summary
plotTiTv(res = titv)

TCGAbiolinks: Searching, downloading and visualizing mutation files

20 March 2019

Search and Download

Mutation data (hg38)

Mutation data (hg19)

Visualize the data