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browsers: + +- Safari (10.0.3) +- Mozilla Firefox (52.0.2) +- Google Chrome (57.0.2987.110) Output - Somatic SNVs/InDels ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -374,51 +376,48 @@ processing with the PCGR annotation pipeline: - GWAS\_CATALOG\_TRAIT\_URI - List of trait URIs for GWAS-associated variant - COSMIC\_MUTATION\_ID - Mutation identifier in `Catalog of somatic - mutations in cancer - COSMIC - v78 `__ + mutations in + cancer `__ database - COSMIC\_CODON\_FRAC\_GW - For different tumor types, number of samples mutated at associated codon position (format: codon\_number:tumor\_type:fraction\_mutated). Samples subject to exome/genome-wide screens only `Catalog of somatic mutations in - cancer - COSMIC - v78 `__. + cancer `__. - COSMIC\_CODON\_COUNT\_GW - For different tumor types, number of samples mutated at associated codon position (format: codon\_number:tumor\_type:frequency). Samples subject to exome/genome-wide screens only `Catalog of somatic mutations in - cancer - COSMIC - v78 `__ + cancer `__ - COSMIC\_COUNT\_GW - Global frequency of variant in `Catalog of - somatic mutations in cancer - COSMIC - v78 `__. + somatic mutations in + cancer `__. - COSMIC\_SITE\_HISTOLOGY - Primary site/histology distribution across - tumor types in `Catalog of somatic mutations in cancer - COSMIC - v78 `__. + tumor types in `Catalog of somatic mutations in + cancer `__. - COSMIC\_CANCER\_TYPE\_GW - Frequency of variant across different - tumor types in `Catalog of somatic mutations in cancer - COSMIC - v78 `__ - - samples subject to exome/genome-wide screens only + tumor types in `Catalog of somatic mutations in + cancer `__ + - samples subject to exome/genome-wide screens only - COSMIC\_CANCER\_TYPE\_ALL - Frequency of variant across different - tumor types in `Catalog of somatic mutations in cancer - COSMIC - v78 `__ + tumor types in `Catalog of somatic mutations in + cancer `__ - COSMIC\_SAMPLE\_SOURCE - Sample source distribution for variant in - `Catalog of somatic mutations in cancer - COSMIC - v78 `__. + `Catalog of somatic mutations in + cancer `__. - COSMIC\_DRUG\_RESISTANCE - Targeted drugs/therapies subject to resistance in tumors that carry the mutation. `Catalog of somatic - mutations in cancer - COSMIC - v78 `__. + mutations in + cancer `__. - COSMIC\_FATHMM\_PRED - Variant effect prediction from COSMIC's FATHMM algorithm (COSMIC variants only) `Catalog of somatic mutations in - cancer - COSMIC - v78 `__. + cancer `__. - COSMIC\_VARTYPE - COSMIC variant type `Catalog of somatic mutations - in cancer - COSMIC - v78 `__. + in + cancer `__. - COSMIC\_CONSEQUENCE - COSMIC consequence type `Catalog of somatic - mutations in cancer - COSMIC - v78 `__. + mutations in + cancer `__. - ICGC\_PROJECTS - Variant frequency count in different `ICGC Project IDs `__ @@ -527,7 +526,7 @@ The following variables are included in the tiered TSV file: particular antineoplastic drug 28. CLINVAR - variant origin and associated traits associated with variant 29. CLINVAR_SIG - clinical significance of CLINVAR variant - 30. GLOBAL_AF_EXAC - adjusted global germline allele frequency in ExAC release 0.3.1 + 30. GLOBAL_AF_EXAC - adjusted global germline allele frequency in ExAC 31. GLOBAL_AF_1KG - 1000G Project - phase 3, germline allele frequency for all 1000G project samples (global) 32. TIER @@ -618,8 +617,8 @@ The format of the compressed TSV file is the following: 13. gene_biotype - type of gene 14. cancer_census_germline - gene implicated with germline predisposition to various cancer subtypes 15. cancer_census_somatic - gene for which somatic mutations have been causally implicated in tumor development - 16. tsgene - tumor suppressor gene status (TSgene 2.0 database) - 17. tsgene_oncogene - oncogene status (TSgene 2.0 database) + 16. tsgene - tumor suppressor gene status (TSgene database) + 17. tsgene_oncogene - oncogene status (TSgene database) 18. intogen_drivers - predicted driver gene status (IntoGen Cancer Drivers Database) 19. antineoplastic_drugs_dgidb - validated and experimental antineoplastic drugs interacting with gene 20. gencode_transcript_type - diff --git a/docs/_build/html/output.html b/docs/_build/html/output.html index 30282680..5dc672dc 100644 --- a/docs/_build/html/output.html +++ b/docs/_build/html/output.html @@ -248,9 +248,12 @@

Output - Interactive HTML reportView an example report for a colorectal tumor sample (TCGA) -

The HTML reports have been tested using the following browsers: * -Safari (10.0.3) * Mozilla Firefox (52.0.2) * Google Chrome -(57.0.2987.110)

+

The HTML reports have been tested using the following browsers:

+
    +
  • Safari (10.0.3)
    • +
  • Mozilla Firefox (52.0.2)
    • +
  • Google Chrome (57.0.2987.110)
    • +

Output - Somatic SNVs/InDelsΒΆ

@@ -532,51 +535,48 @@

Variant frequencies/annotations in germline/somatic databasesGWAS_CATALOG_TRAIT_URI - List of trait URIs for GWAS-associated variant
  • COSMIC_MUTATION_ID - Mutation identifier in Catalog of somatic -mutations in cancer - COSMIC -v78 +mutations in +cancer database
  • COSMIC_CODON_FRAC_GW - For different tumor types, number of samples mutated at associated codon position (format: codon_number:tumor_type:fraction_mutated). Samples subject to exome/genome-wide screens only Catalog of somatic mutations in -cancer - COSMIC -v78.
    • +cancer.
  • COSMIC_CODON_COUNT_GW - For different tumor types, number of samples mutated at associated codon position (format: codon_number:tumor_type:frequency). Samples subject to exome/genome-wide screens only Catalog of somatic mutations in -cancer - COSMIC -v78
    • +cancer
  • COSMIC_COUNT_GW - Global frequency of variant in Catalog of -somatic mutations in cancer - COSMIC -v78.
    • +somatic mutations in +cancer.
  • COSMIC_SITE_HISTOLOGY - Primary site/histology distribution across -tumor types in Catalog of somatic mutations in cancer - COSMIC -v78.
    • +tumor types in Catalog of somatic mutations in +cancer.
  • COSMIC_CANCER_TYPE_GW - Frequency of variant across different -tumor types in Catalog of somatic mutations in cancer - COSMIC -v78 - -samples subject to exome/genome-wide screens only
    • +tumor types in Catalog of somatic mutations in +cancer +- samples subject to exome/genome-wide screens only
  • COSMIC_CANCER_TYPE_ALL - Frequency of variant across different -tumor types in Catalog of somatic mutations in cancer - COSMIC -v78
    • +tumor types in Catalog of somatic mutations in +cancer
  • COSMIC_SAMPLE_SOURCE - Sample source distribution for variant in -Catalog of somatic mutations in cancer - COSMIC -v78.
    • +Catalog of somatic mutations in +cancer.
  • COSMIC_DRUG_RESISTANCE - Targeted drugs/therapies subject to resistance in tumors that carry the mutation. Catalog of somatic -mutations in cancer - COSMIC -v78.
    • +mutations in +cancer.
  • COSMIC_FATHMM_PRED - Variant effect prediction from COSMIC’s FATHMM algorithm (COSMIC variants only) Catalog of somatic mutations in -cancer - COSMIC -v78.
    • +cancer.
  • COSMIC_VARTYPE - COSMIC variant type Catalog of somatic mutations -in cancer - COSMIC -v78.
    • +in +cancer.
  • COSMIC_CONSEQUENCE - COSMIC consequence type Catalog of somatic -mutations in cancer - COSMIC -v78.
    • +mutations in +cancer.
  • ICGC_PROJECTS - Variant frequency count in different ICGC Project IDs
    • @@ -681,7 +681,7 @@

    Annotated List of all SNVs/InDelsparticular antineoplastic drug 28. CLINVAR - variant origin and associated traits associated with variant 29. CLINVAR_SIG - clinical significance of CLINVAR variant -30. GLOBAL_AF_EXAC - adjusted global germline allele frequency in ExAC release 0.3.1 +30. GLOBAL_AF_EXAC - adjusted global germline allele frequency in ExAC 31. GLOBAL_AF_1KG - 1000G Project - phase 3, germline allele frequency for all 1000G project samples (global) 32. TIER @@ -761,8 +761,8 @@

    1. Tab-separated values (TSV)13. gene_biotype - type of gene 14. cancer_census_germline - gene implicated with germline predisposition to various cancer subtypes 15. cancer_census_somatic - gene for which somatic mutations have been causally implicated in tumor development -16. tsgene - tumor suppressor gene status (TSgene 2.0 database) -17. tsgene_oncogene - oncogene status (TSgene 2.0 database) +16. tsgene - tumor suppressor gene status (TSgene database) +17. tsgene_oncogene - oncogene status (TSgene database) 18. intogen_drivers - predicted driver gene status (IntoGen Cancer Drivers Database) 19. antineoplastic_drugs_dgidb - validated and experimental antineoplastic drugs interacting with gene 20. gencode_transcript_type - diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js index 332c867e..08114d90 100644 --- a/docs/_build/html/searchindex.js +++ b/docs/_build/html/searchindex.js @@ -1 +1 @@ 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index dcf216ae..a99676a6 100644 --- a/docs/output.md +++ b/docs/output.md @@ -51,11 +51,11 @@ The __sample_id__ is provided as input by the user, and reflects a unique identi * [View an example report for a colorectal tumor sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.COAD.pcgr.html) The HTML reports have been tested using the following browsers: + * Safari (10.0.3) * Mozilla Firefox (52.0.2) * Google Chrome (57.0.2987.110) - ### Output - Somatic SNVs/InDels #### Variant call format - VCF @@ -181,18 +181,18 @@ Here, the __sample_id__ is provided as input by the user, and reflects a unique - DBSNP_SUBMISSIONS - Number of individual submissions to rsID - GWAS\_CATALOG_PMID - Variant is linked to phenotype through the [GWAS Catalog](https://www.ebi.ac.uk/gwas/), literature in PMID list - GWAS\_CATALOG\_TRAIT_URI - List of trait URIs for GWAS-associated variant - - COSMIC\_MUTATION_ID - Mutation identifier in [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/) database - - COSMIC\_CODON\_FRAC\_GW - For different tumor types, number of samples mutated at associated codon position (format: codon\_number:tumor\_type:fraction_mutated). Samples subject to exome/genome-wide screens only [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). - - COSMIC\_CODON\_COUNT\_GW - For different tumor types, number of samples mutated at associated codon position (format: codon\_number:tumor\_type:frequency). Samples subject to exome/genome-wide screens only [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/) - - COSMIC\_COUNT\_GW - Global frequency of variant in [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). - - COSMIC\_SITE\_HISTOLOGY - Primary site/histology distribution across tumor types in [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). - - COSMIC\_CANCER\_TYPE\_GW - Frequency of variant across different tumor types in [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/) - samples subject to exome/genome-wide screens only - - COSMIC\_CANCER\_TYPE\_ALL - Frequency of variant across different tumor types in [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/) - - COSMIC\_SAMPLE\_SOURCE - Sample source distribution for variant in [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). - - COSMIC\_DRUG\_RESISTANCE - Targeted drugs/therapies subject to resistance in tumors that carry the mutation. [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). - - COSMIC\_FATHMM\_PRED - Variant effect prediction from COSMIC's FATHMM algorithm (COSMIC variants only) [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). - - COSMIC_VARTYPE - COSMIC variant type [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). - - COSMIC_CONSEQUENCE - COSMIC consequence type [Catalog of somatic mutations in cancer - COSMIC v78](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). + - COSMIC\_MUTATION_ID - Mutation identifier in [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/) database + - COSMIC\_CODON\_FRAC\_GW - For different tumor types, number of samples mutated at associated codon position (format: codon\_number:tumor\_type:fraction_mutated). Samples subject to exome/genome-wide screens only [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). + - COSMIC\_CODON\_COUNT\_GW - For different tumor types, number of samples mutated at associated codon position (format: codon\_number:tumor\_type:frequency). Samples subject to exome/genome-wide screens only [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/) + - COSMIC\_COUNT\_GW - Global frequency of variant in [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). + - COSMIC\_SITE\_HISTOLOGY - Primary site/histology distribution across tumor types in [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). + - COSMIC\_CANCER\_TYPE\_GW - Frequency of variant across different tumor types in [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/) - samples subject to exome/genome-wide screens only + - COSMIC\_CANCER\_TYPE\_ALL - Frequency of variant across different tumor types in [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/) + - COSMIC\_SAMPLE\_SOURCE - Sample source distribution for variant in [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). + - COSMIC\_DRUG\_RESISTANCE - Targeted drugs/therapies subject to resistance in tumors that carry the mutation. [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). + - COSMIC\_FATHMM\_PRED - Variant effect prediction from COSMIC's FATHMM algorithm (COSMIC variants only) [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). + - COSMIC_VARTYPE - COSMIC variant type [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). + - COSMIC_CONSEQUENCE - COSMIC consequence type [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). - ICGC_PROJECTS - Variant frequency count in different [ICGC Project IDs](https://dcc.icgc.org/repository/current/Projects) @@ -272,7 +272,7 @@ The following variables are included in the tiered TSV file: particular antineoplastic drug 28. CLINVAR - variant origin and associated traits associated with variant 29. CLINVAR_SIG - clinical significance of CLINVAR variant - 30. GLOBAL_AF_EXAC - adjusted global germline allele frequency in ExAC release 0.3.1 + 30. GLOBAL_AF_EXAC - adjusted global germline allele frequency in ExAC 31. GLOBAL_AF_1KG - 1000G Project - phase 3, germline allele frequency for all 1000G project samples (global) 32. TIER @@ -342,8 +342,8 @@ The format of the compressed TSV file is the following: 13. gene_biotype - type of gene 14. cancer_census_germline - gene implicated with germline predisposition to various cancer subtypes 15. cancer_census_somatic - gene for which somatic mutations have been causally implicated in tumor development - 16. tsgene - tumor suppressor gene status (TSgene 2.0 database) - 17. tsgene_oncogene - oncogene status (TSgene 2.0 database) + 16. tsgene - tumor suppressor gene status (TSgene database) + 17. tsgene_oncogene - oncogene status (TSgene database) 18. intogen_drivers - predicted driver gene status (IntoGen Cancer Drivers Database) 19. antineoplastic_drugs_dgidb - validated and experimental antineoplastic drugs interacting with gene 20. gencode_transcript_type - diff --git a/docs/output.rst b/docs/output.rst index 15fd8c9e..a83e3ae1 100644 --- a/docs/output.rst +++ b/docs/output.rst @@ -89,9 +89,11 @@ unique identifier of the tumor-normal sample pair to be analyzed. - `View an example report for a colorectal tumor sample (TCGA) `__ -The HTML reports have been tested using the following browsers: \* -Safari (10.0.3) \* Mozilla Firefox (52.0.2) \* Google Chrome -(57.0.2987.110) +The HTML reports have been tested using the following browsers: + +- Safari (10.0.3) +- Mozilla Firefox (52.0.2) +- Google Chrome (57.0.2987.110) Output - Somatic SNVs/InDels ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -374,51 +376,48 @@ processing with the PCGR annotation pipeline: - GWAS\_CATALOG\_TRAIT\_URI - List of trait URIs for GWAS-associated variant - COSMIC\_MUTATION\_ID - Mutation identifier in `Catalog of somatic - mutations in cancer - COSMIC - v78 `__ + mutations in + cancer `__ database - COSMIC\_CODON\_FRAC\_GW - For different tumor types, number of samples mutated at associated codon position (format: codon\_number:tumor\_type:fraction\_mutated). Samples subject to exome/genome-wide screens only `Catalog of somatic mutations in - cancer - COSMIC - v78 `__. + cancer `__. - COSMIC\_CODON\_COUNT\_GW - For different tumor types, number of samples mutated at associated codon position (format: codon\_number:tumor\_type:frequency). Samples subject to exome/genome-wide screens only `Catalog of somatic mutations in - cancer - COSMIC - v78 `__ + cancer `__ - COSMIC\_COUNT\_GW - Global frequency of variant in `Catalog of - somatic mutations in cancer - COSMIC - v78 `__. + somatic mutations in + cancer `__. - COSMIC\_SITE\_HISTOLOGY - Primary site/histology distribution across - tumor types in `Catalog of somatic mutations in cancer - COSMIC - v78 `__. + tumor types in `Catalog of somatic mutations in + cancer `__. - COSMIC\_CANCER\_TYPE\_GW - Frequency of variant across different - tumor types in `Catalog of somatic mutations in cancer - COSMIC - v78 `__ - - samples subject to exome/genome-wide screens only + tumor types in `Catalog of somatic mutations in + cancer `__ + - samples subject to exome/genome-wide screens only - COSMIC\_CANCER\_TYPE\_ALL - Frequency of variant across different - tumor types in `Catalog of somatic mutations in cancer - COSMIC - v78 `__ + tumor types in `Catalog of somatic mutations in + cancer `__ - COSMIC\_SAMPLE\_SOURCE - Sample source distribution for variant in - `Catalog of somatic mutations in cancer - COSMIC - v78 `__. + `Catalog of somatic mutations in + cancer `__. - COSMIC\_DRUG\_RESISTANCE - Targeted drugs/therapies subject to resistance in tumors that carry the mutation. `Catalog of somatic - mutations in cancer - COSMIC - v78 `__. + mutations in + cancer `__. - COSMIC\_FATHMM\_PRED - Variant effect prediction from COSMIC's FATHMM algorithm (COSMIC variants only) `Catalog of somatic mutations in - cancer - COSMIC - v78 `__. + cancer `__. - COSMIC\_VARTYPE - COSMIC variant type `Catalog of somatic mutations - in cancer - COSMIC - v78 `__. + in + cancer `__. - COSMIC\_CONSEQUENCE - COSMIC consequence type `Catalog of somatic - mutations in cancer - COSMIC - v78 `__. + mutations in + cancer `__. - ICGC\_PROJECTS - Variant frequency count in different `ICGC Project IDs `__ @@ -527,7 +526,7 @@ The following variables are included in the tiered TSV file: particular antineoplastic drug 28. CLINVAR - variant origin and associated traits associated with variant 29. CLINVAR_SIG - clinical significance of CLINVAR variant - 30. GLOBAL_AF_EXAC - adjusted global germline allele frequency in ExAC release 0.3.1 + 30. GLOBAL_AF_EXAC - adjusted global germline allele frequency in ExAC 31. GLOBAL_AF_1KG - 1000G Project - phase 3, germline allele frequency for all 1000G project samples (global) 32. TIER @@ -618,8 +617,8 @@ The format of the compressed TSV file is the following: 13. gene_biotype - type of gene 14. cancer_census_germline - gene implicated with germline predisposition to various cancer subtypes 15. cancer_census_somatic - gene for which somatic mutations have been causally implicated in tumor development - 16. tsgene - tumor suppressor gene status (TSgene 2.0 database) - 17. tsgene_oncogene - oncogene status (TSgene 2.0 database) + 16. tsgene - tumor suppressor gene status (TSgene database) + 17. tsgene_oncogene - oncogene status (TSgene database) 18. intogen_drivers - predicted driver gene status (IntoGen Cancer Drivers Database) 19. antineoplastic_drugs_dgidb - validated and experimental antineoplastic drugs interacting with gene 20. gencode_transcript_type -