lmabrasil-hg38

Versão Reduzida no Google Colab:

Workflow

Filtrar variantes somáticas - Workflow

Clonar repositório renatopuga/lmabrasil-hg38
Instalar bcftools +split-vep
Instalar udocker
Filtrar o VCF com filter_vep:

-filter "(MAX_AF <= 0.01 or not MAX_AF) and
(FILTER = PASS or not FILTER matches strand_bias,weak_evidence) and
(SOMATIC matches 1 or (not SOMATIC and CLIN_SIG matches pathogenic)) and
(not CLIN_SIG matches benign) and \
(not IMPACT matches LOW) and \
(Symbol in hpo/$HPO)

Filtrar Cobertura Total e Frequência Alélica da variante com: bcftools +split-vep:

DP>=20 AND AF>=0.1

Resultado: *.vep.filter.tsv

The Human Phenotype Ontology (HPO)

Myelofibrosis: https://hpo.jax.org/app/browse/term/HP:0011974
Abnormal mast cell morphology: https://hpo.jax.org/app/browse/term/HP:0100494

Clonal Hematopoiesis drivers

Clonal Hematopoiesis drivers (65 genes): https://www.intogen.org/ch

vep.sh - script

Rodar script VEP completo (vep annot + vep_filter)

sh vep.sh WP017 Myelofibrosis.txt

Rodar script VEP no Google Colab (vep_filter)

sh vep-gc.sh WP017 Myelofibrosis.txt

output - .vep.filter.tsv

Sobre a amostra WP017.

Class: Myelofibrosis
Information: JAK2-
Total de variantes no VCF: 7144
Total de variantes pós filtro: 2

CHROM	POS	REF	ALT	Location	SYMBOL	Consequence	Feature	MANE_SELECT	BIOTYPE	HGVSc	HGVSp	EXON	INTRON	VARIANT_CLASS	SIFT	PolyPhen	gnomADg_AF	MAX_AF	IMPACT	CLIN_SIG	SOMATIC	Existing_variation	FILTER	TumorID	GT	DP	AD	AF	NormalID	NGT	NDP	NAD	NAF
chr17	7669662	T	G	chr17:7669662	TP53	missense_variant	NM_000546.6	ENST00000269305.9	protein_coding	NM_000546.6:c.1129A>C	NP_000537.3:p.Thr377Pro	11/11	.	SNV	tolerated(0.42)	.	0.000053	0.000496	MODERATE	uncertain_significance	0&1	rs774269719&COSV52716766	base_qual;haplotype;normal_artifact;strand_bias	WP017	0\|1	119	101,18	0.112	WP018	0\|0	60	55,5	0.049
chr19	12943750	GCAGAGGCTTAAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGAGGAG	A	chr19:12943751-12943802	CALR	frameshift_variant	NM_004343.4	ENST00000316448.10	protein_coding	NM_004343.4:c.1099_1150del	NP_004334.1:p.Leu367ThrfsTer46	9/9	.	deletion	.	.	0.000020	0.000066	HIGH	pathogenic	.	rs1555760738	PASS	WP017	0/1	102	62,40	0.416	WP018	0/0	50	50,0	0.022

Cancer Genome Interpreter

https://www.cancergenomeinterpreter.org/analysis

CGI - Resultado Resumido

chr	pos	alt	STRAND	CGI-Gene	ALT_TYPE	CGI-Oncogenic Prediction
chr17	7669662	G	+	TP53	snp	passenger (oncodriveMUT)
chr19	12943750	A	+	CALR	indel	driver (oncodriveMUT)

CGI - resultado Completo

CHROMOSOME	POSITION	REF	ALT	chr	pos	ref	alt	ALT_TYPE	STRAND	CGI-Sample ID	CGI-Gene	CGI-Protein Change	CGI-Oncogenic Summary	CGI-Oncogenic Prediction	CGI-External oncogenic annotation	CGI-Mutation	CGI-Consequence	CGI-Transcript	CGI-STRAND	CGI-Type	CGI-HGVS	CGI-HGVSc	CGI-HGVSp
17	7669662	T	G	chr17	7669662	T	G	snp	+	input_gtf	TP53	T377P	non-oncogenic	passenger (oncodriveMUT)		chr17:7669662 T>G	missense_variant	ENST00000269305	+	SNV	ENST00000269305:c.1129A>C;p.(Thr377Pro);p.(T377P)	ENST00000269305.9:c.1129A>C	ENSP00000269305.4:p.Thr377Pro
19	12943751	GCAGAGGCTTAAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGAGGAG	-	chr19	12943750	AGCAGAGGCTTAAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGAGGAG	A	indel	+	input_gtf	CALR	EQRLKEEEEDKKRKEEEE364-381X	oncogenic (predicted and annotated)	driver (oncodriveMUT)	clinvar:97006	chr19:12943751-12943751 GCAGAGGCTTAAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGAGGAG>-	frameshift_variant	ENST00000316448	+	DEL	ENST00000316448:c.1099_1150del;p.(Leu367ThrfsTer46);p.(L367Tfs*46)	ENST00000316448.10:c.1099_1150del	ENSP00000320866.4:p.Leu367ThrfsTer46

Usando CGI via API Rest no Google Colab

Cancer Genome Interpreter (CGI) - API

Utilizando o resultado da amostra WP048, vamos utilizar a análise do CGI através da API Rest que eles disponibilizam. Para mais informações sobre a API Rest do CGI acesse: https://www.cancergenomeinterpreter.org/rest_api

Requisitos para acessar a API:

Conta de usuário no CGI
Gerar um token para utilizar no código que chama a API (exemplo abaixo)

Gerando Token no seu usuário CGI

Gerando o arquivo df_WP048-cgi.txt com as colunas: CHR, POS, REF e ALT. Esse arquivo será utilizando junto com a API.

Nota: Os nomes das colunas, para esse formato que estamos utilizando de input, deve ser exatamente CHR, POS, REF e ALT.

%%bash
cut -f1-4 /content/lmabrasil-hg38/vep_output/liftOver_WP048_hg19ToHg38.vep.filter.tsv | sed -e "s/CHROM/CHR/g"  > df_WP048-cgi.txt
head df_WP048-cgi.txt

Enviando um Job - job_id: be69dc21d218f22e5f7e

IMPORTANTE: No código, onde estiver escrito: SEU_TOKEN, é para colar o seu código Token. Linha de código:

headers = {'Authorization': '[email protected] SEU_TOKEN'}

IMPORTANTE 2: O jobid cb99f036442f7b74f195 é válido, eu gerei usando o meu Token.

import requests
headers = {'Authorization': '[email protected] SEU_TOKEN'}
payload = {'cancer_type': 'HEMATO', 'title': 'Somatic MF', 'reference': 'hg38'}
r = requests.post('https://www.cancergenomeinterpreter.org/api/v1',
                headers=headers,
                files={
                        'mutations': open('/content/df_WP048-cgi.txt', 'rb')
                        },
                data=payload)
r.json()

be69dc21d218f22e5f7e

Visualizando os identificadores

import requests
job_id ="be69dc21d218f22e5f7e"

headers = {'Authorization': '[email protected] SEU_TOKEN'}
r = requests.get('https://www.cancergenomeinterpreter.org/api/v1/%s' % job_id, headers=headers)
r.json()

{'status': 'Done',
 'metadata': {'id': 'be69dc21d218f22e5f7e',
  'user': '[email protected]',
  'title': 'Somatic MF',
  'cancertype': 'HEMATO',
  'reference': 'hg38',
  'dataset': 'input.tsv',
  'date': '2024-01-05 15:01:08'}}

Acessando informações do Job

import requests
job_id ="be69dc21d218f22e5f7e"

headers = {'Authorization': '[email protected] SEU_TOKEN'}
payload={'action':'logs'}
r = requests.get('https://www.cancergenomeinterpreter.org/api/v1/%s' % job_id, headers=headers, params=payload)
r.json()

{'status': 'Done',
 'logs': ['# cgi analyze input.tsv -c HEMATO -g hg38',
  '2024-01-05 16:01:13,170 INFO     Parsing input01.tsv\n',
  '2024-01-05 16:01:17,258 INFO     Running VEP\n',
  '2024-01-05 16:01:18,446 INFO     Check cancer genes and consensus roles\n',
  '2024-01-05 16:01:18,535 INFO     Annotate BoostDM mutations\n',
  '2024-01-05 16:01:18,572 INFO     Annotate OncodriveMUT mutations\n',
  '2024-01-05 16:01:21,180 INFO     Annotate validated oncogenic mutations\n',
  '2024-01-05 16:01:21,375 INFO     Check oncogenic classification\n',
  '2024-01-05 16:01:21,442 INFO     Matching biomarkers\n',
  '2024-01-05 16:01:21,535 INFO     Prescription finished\n',
  '2024-01-05 16:01:21,548 INFO     Aggregate metrics\n',
  '2024-01-05 16:01:24,808 INFO     Compress output files\n',
  '2024-01-05 16:01:24,846 INFO     Analysis done\n']}

Download dos Resultados (file.zip)

import requests
job_id ="be69dc21d218f22e5f7e"

headers = {'Authorization': '[email protected] SEU_TOKEN'}
payload={'action':'download'}
r = requests.get('https://www.cancergenomeinterpreter.org/api/v1/%s' % job_id, headers=headers, params=payload)
with open('file.zip', 'wb') as fd:
    fd.write(r._content)

Descompactando o arquivo `file.zip`

!unzip file.zip

Archive:  file.zip
  inflating: alterations.tsv         
  inflating: biomarkers.tsv          
  inflating: input01.tsv             
  inflating: summary.txt

Resultado: `alterations.tsv`

pd.read_csv('/content/alterations.tsv',sep='\t',index_col=False, engine= 'python')

Input ID	CHROMOSOME	POSITION	REF	ALT	CHR	POS	ALT_TYPE	STRAND	CGI-Sample ID	CGI-Gene	CGI-Protein Change	CGI-Oncogenic Summary	CGI-Oncogenic Prediction	CGI-External oncogenic annotation	CGI-Mutation	CGI-Consequence	CGI-Transcript	CGI-STRAND	CGI-Type	CGI-HGVS	CGI-HGVSc	CGI-HGVSp
0	input01_1	1	114716123	C	T	chr1	114716123	snp	+	input01	NRAS	G13D	oncogenic (predicted and annotated)	driver (boostDM: non-tissue-specific model)	cgi,oncokb	chr1:114716123 C>T	missense_variant	ENST00000369535	+	SNV	ENST00000369535:c.38G>A;p.(Gly13Asp);p.(G13D)	ENST00000369535.5:c.38G>A	ENSP00000358548.4:p.Gly13Asp
1	input01_2	9	5073770	G	T	chr9	5073770	snp	+	input01	JAK2	V617F	oncogenic (annotated)	passenger (oncodriveMUT)	cgi,oncokb	chr9:5073770 G>T	missense_variant	ENST00000381652	+	SNV	ENST00000381652:c.1849G>T;p.(Val617Phe);p.(V617F)	ENST00000381652.4:c.1849G>T	ENSP00000371067.4:p.Val617Phe

Resultado: `biomarkers.tsv`

pd.read_csv('/content/biomarkers.tsv',sep='\t',index_col=False, engine= 'python')

Sample ID	Alterations	Biomarker	Drugs	Diseases	Response	Evidence	Match	Source	BioM	Resist.	Tumor type
0	input01	KRAS wildtype	KRAS wildtype	Panitumumab (EGFR mAb inhibitor)	Colorectal adenocarcinoma	Responsive	A	NO	PMID: 31268481	complete	621.0	COREAD
1	input01	KRAS wildtype	KRAS wildtype	Cetuximab (EGFR mAb inhibitor)	Colorectal adenocarcinoma	Responsive	A	NO	PMID: 19339720	complete	246.0	COREAD
2	input01	JAK2 (V617F)	JAK2 oncogenic mutation	PD1 inhibitors	Cutaneous melanoma	Resistant	C	NO	PMID:27433843	complete	NaN	CM
3	input01	NRAS (G13D)	NRAS (12,13,59,61,117,146)	Cetuximab (EGFR mAb inhibitor)	Colorectal adenocarcinoma	Resistant	A	NO	PMID:24024839;PMID:20619739;PMID:23325582	complete	NaN	COREAD
4	input01	NRAS (G13D)	NRAS (Q61)	BRAF inhibitors	Cutaneous melanoma	Resistant	C	NO	PMID:23569304;PMID:24265153	only alteration type	NaN	CM
5	input01	JAK2 (V617F)	JAK2 (V617F)	JAK inhibitor (alone or in combination)s	Acute myeloid leukemia	Responsive	D	YES	PMID:22829971	complete	NaN	AML
6	input01	JAK2 (V617F)	JAK2 amplification	JAK inhibitors	Breast adenocarcinoma	Responsive	D	NO	PMID:27075627	only gene	NaN	BRCA
7	input01	NRAS (G13D)	NRAS (12,13,59,61,117,146)	Panitumumab (EGFR mAb inhibitor)	Colorectal adenocarcinoma	Resistant	A	NO	FDA guidelines	complete	NaN	COREAD
8	input01	JAK2 (V617F)	JAK2-BRAF fusion	Ruxolitinib (JAK inhibitor)	Acute lymphoblastic leukemia	Responsive	D	YES	PMID:22875628;PMID:22899477	only gene	NaN	ALL
9	input01	JAK2 (V617F)	JAK2 (V617F)	Ruxolitinib (JAK inhibitor)	Acute myeloid leukemia	Responsive	C	YES	PMID:22422826	complete	NaN	AML
10	input01	JAK2 (V617F)	JAK2 (V617F)	Ruxolitinib (JAK inhibitor)	Myelofibrosis	Responsive	A	YES	FDA	complete	NaN	MY
11	input01	KIT wildtype	KIT wildtype	Dasatinib (BCR-ABL inhibitor 2nd gen)	Gastrointestinal stromal	Responsive	D	NO	PMID:16397263	complete	NaN	GIST
12	input01	KIT wildtype	KIT wildtype	Sorafenib (Pan-TK inhibitor)	Gastrointestinal stromal	Responsive	C	NO	ASCO 2011 (abstr 10009)	complete	NaN	GIST
13	input01	KIT wildtype	KIT wildtype	Sunitinib (Pan-TK inhibitor)	Gastrointestinal stromal	Responsive	B	NO	PMID:18955458	complete	NaN	GIST
14	input01	KIT wildtype	KIT wildtype	Imatinib (BCR-ABL inhibitor 1st gen&KIT inhibitor)	Gastrointestinal stromal	Resistant	B	NO	PMID:18955458	complete	NaN	GIST
15	input01	PDGFRA wildtype	PDGFRA wildtype	Imatinib (BCR-ABL inhibitor 1st gen&KIT inhibitor)	Gastrointestinal stromal	Resistant	B	NO	PMID:14645423;PMID:18955458	complete	NaN	GIST
16	input01	NRAS (G13D)	NRAS oncogenic mutation	CDK4/6 inhibitor + MEK inhibitors	Cutaneous melanoma	Responsive	C	NO	PMID:26658964;NCT01781572;NCT02065063;NCT02022982;ASCO 2014 (abstr 9009)	complete	NaN	CM
17	input01	NRAS (G13D)	NRAS (G12C)	ERK inhibitors	Any cancer type	Responsive	D	YES	PMID:23614898	only alteration type	NaN	CANCER
18	input01	NRAS (G13D)	NRAS oncogenic mutation	ERK inhibitors	Cutaneous melanoma	Responsive	C	NO	ASCO 2017 (abstr 2508)	complete	NaN	CM
19	input01	NRAS (G13D)	NRAS oncogenic mutation	HSP90 inhibitors	Cutaneous melanoma	Responsive	D	NO	PMID:23538902	complete	NaN	CM
20	input01	NRAS (G13D)	NRAS oncogenic mutation	MEK inhibitor +/- PI3K pathway inhibitors	Colorectal adenocarcinoma	Responsive	D	NO	PMID:23274911;PMID:22392911	complete	NaN	COREAD
21	input01	NRAS (G13D)	NRAS oncogenic mutation	MEK inhibitors	Acute myeloid leukemia, Lung adenocarcinoma, Acute lymphoblastic leukemia	Responsive	D	YES	PMID:22507781;PMID:23515407;PMID:18701506	complete	NaN	AML, LUAD, ALL
22	input01	NRAS (G13D)	NRAS (Q61)	MEK inhibitors	Cutaneous melanoma	Responsive	B	NO	PMID:23414587,ASCO 2016 (abstr 9500)	only alteration type	NaN	CM
23	input01	NRAS (G13D)	NRAS oncogenic mutation	Pan-RAF inhibitors	Cutaneous melanoma	Responsive	C	NO	ESMO 2015 (abstract 300);AACR 2017 (abstr CT002)	complete	NaN	CM
24	input01	NRAS (G13D)	NRAS oncogenic mutation	PI3K pathway inhibitor + MEK inhibitors	Myeloma	Responsive	D	YES	PMID:22985491	complete	NaN	MYMA
25	input01	NRAS (G13D)	NRAS oncogenic mutation	Sorafenib + MEK inhibitor (Pan-TK inhibitor + MEK inhibitor)	Hepatic carcinoma	Responsive	C	NO	PMID:25294897	complete	NaN	HC
26	input01	PDGFRA wildtype	PDGFRA wildtype	Dasatinib (BCR-ABL inhibitor 2nd gen)	Gastrointestinal stromal	Responsive	D	NO	PMID:16397263	complete	NaN	GIST
27	input01	PDGFRA wildtype	PDGFRA wildtype	Sorafenib (Pan-TK inhibitor)	Gastrointestinal stromal	Responsive	C	NO	ASCO 2011 (abstr 10009)	complete	NaN	GIST
28	input01	PDGFRA wildtype	PDGFRA wildtype	Sunitinib (Pan-TK inhibitor)	Gastrointestinal stromal	Responsive	B	NO	PMID:18955458	complete	NaN	GIST
29	input01	TP53 wildtype	TP53 wildtype	HDM2 inhibitors	Acute myeloid leukemia	Responsive	C	YES	AACR 2017 (abstr CT152)	complete	NaN	AML
30	input01	NRAS (G13D)	NRAS oncogenic mutation	Vemurafenib (BRAF inhibitor)	Cutaneous melanoma	Resistant	D	NO	PMID:20179705	complete	NaN	CM
31	input01	NRAS (G13D)	NRAS (Q61K,T50I,G13D,G60E,G12C,G12V,T58I,.,Q61H,G12R,G12D,Q61L,G13V,Q61R)	Panitumumab + Cetuximab	Colorectal adenocarcinoma	Resistant	A	NO	oncokb: oncokb=https://www.oncokb.org/gene/NRAS	complete	NaN	COREAD
32	input01	NRAS (G13D)	NRAS (Q61K,T50I,G13D,G60E,G12C,G12V,T58I,.,Q61H,G12R,G12D,Q61L,G13V,Q61R)	Binimetinib + Binimetinib + Ribociclib	Cutaneous melanoma	Responsive	C	NO	oncokb: oncokb=https://www.oncokb.org/gene/NRAS	complete	NaN	CM
33	input01	JAK2 (V617F)	JAK2-PCM1 fusion	Ruxolitinib	Eosinophilic chronic leukemia	Responsive	C	YES	oncokb: oncokb=https://www.oncokb.org/gene/JAK2	only gene	NaN	ECL
34	input01	NRAS (G13D)	NRAS (Q61K,T50I,G13D,G60E,G12C,G12V,T58I,.,Q61H,G12R,G12D,Q61L,G13V,Q61R)	Selumetinib	Thyroid carcinoma	Responsive	C	NO	oncokb: oncokb=https://www.oncokb.org/gene/NRAS	complete	NaN	THCA
35	input01	BRAF wildtype	BRAF WILD TYPE	MEK Inhibitor RO4987655	Cutaneous melanoma	Resistant	B	NO	https://civicdb.org/links/molecular_profiles/422	complete	NaN	CM
36	input01	EGFR wildtype	EGFR Wildtype	Gefitinib	Non-small cell lung	Resistant	B	NO	https://civicdb.org/links/molecular_profiles/2050	complete	NaN	NSCLC
37	input01	JAK2 (V617F)	JAK2 Splice Site (c.1641+2T>G)	Pembrolizumab	Cutaneous melanoma	Resistant	C	NO	https://civicdb.org/links/molecular_profiles/1589	only alteration type	NaN	CM
38	input01	KIT wildtype	KIT WILDTYPE	Regorafenib	Gastrointestinal stromal	Response	B	NO	https://civicdb.org/links/molecular_profiles/2520	complete	NaN	GIST
39	input01	NRAS (G13D)	NRAS G13D	Tanespimycin	Cutaneous melanoma	Response	C	NO	https://civicdb.org/links/molecular_profiles/93	complete	NaN	CM
40	input01	NRAS (G13D)	NRAS Mutation	MEK Inhibitor RO4987655	Cutaneous melanoma	Resistant	C	NO	https://civicdb.org/links/molecular_profiles/208	complete	NaN	CM
41	input01	NRAS (G13D)	NRAS Mutation	Dabrafenib,Vemurafenib	Cutaneous melanoma	Resistant	B	NO	https://civicdb.org/links/molecular_profiles/208	complete	NaN	CM
42	input01	NRAS (G13D)	NRAS Mutation	Trametinib	Cutaneous melanoma	Response	B	NO	https://civicdb.org/links/molecular_profiles/208	complete	NaN	CM
43	input01	NRAS (G13D)	NRAS Mutation	Trametinib,Omipalisib	Cutaneous melanoma	Response	D	NO	https://civicdb.org/links/molecular_profiles/208	complete	NaN	CM
44	input01	NRAS (G13D)	NRAS Mutation	Binimetinib	Cutaneous melanoma	Response	D	NO	https://civicdb.org/links/molecular_profiles/208	complete	NaN	CM
45	input01	NRAS (G13D)	NRAS Q61	Vemurafenib	Cutaneous melanoma	Resistant	B	NO	https://civicdb.org/links/molecular_profiles/94	only alteration type	NaN	CM
46	input01	NRAS (G13D)	NRAS Q61K	Binimetinib,Everolimus	Neuroblastoma	Response	D	NO	https://civicdb.org/links/molecular_profiles/423	only alteration type	NaN	NB
47	input01	NRAS (G13D)	NRAS Q61K	Trametinib,Selumetinib	Non-small cell lung	Response	D	NO	https://civicdb.org/links/molecular_profiles/423	only alteration type	NaN	NSCLC
48	input01	NRAS (G13D)	NRAS Q61L	Temozolomide	Cutaneous melanoma	Response	C	NO	https://civicdb.org/links/molecular_profiles/95	only alteration type	NaN	CM
49	input01	NRAS (G13D)	NRAS Q61R	Temozolomide	Cutaneous melanoma	Response	C	NO	https://civicdb.org/links/molecular_profiles/96	only alteration type	NaN	CM
50	input01	TP53 wildtype	TP53 Wildtype	Adjuvant Chemotherapy	Non-small cell lung	Response	B	NO	https://civicdb.org/links/molecular_profiles/365	complete	NaN	NSCLC

Deletando o Job do CGI

import requests
#job_id ="be69dc21d218f22e5f7e"

headers = {'Authorization': '[email protected] SEU_TOKEN'}
r = requests.delete('https://www.cancergenomeinterpreter.org/api/v1/%s' % job_id, headers=headers)
r.json()

Name		Name	Last commit message	Last commit date
Latest commit History 61 Commits
hpo		hpo
vep_output		vep_output
README.md		README.md
WP017.filtered.chr.vcf.gz		WP017.filtered.chr.vcf.gz
WP017.filtered.chr.vcf.gz.tbi		WP017.filtered.chr.vcf.gz.tbi
WP019.filtered.chr.vcf.gz		WP019.filtered.chr.vcf.gz
WP019.filtered.chr.vcf.gz.tbi		WP019.filtered.chr.vcf.gz.tbi
WP058.filtered.chr.vcf.gz		WP058.filtered.chr.vcf.gz
WP058.filtered.chr.vcf.gz.tbi		WP058.filtered.chr.vcf.gz.tbi
WP068.filtered.chr.vcf.gz		WP068.filtered.chr.vcf.gz
WP068.filtered.chr.vcf.gz.tbi		WP068.filtered.chr.vcf.gz.tbi
hg19ToHg38.over.chain		hg19ToHg38.over.chain
liftOver_WP017_hg19ToHg38.vcf.gz		liftOver_WP017_hg19ToHg38.vcf.gz
liftOver_WP017_hg19ToHg38.vcf.gz.tbi		liftOver_WP017_hg19ToHg38.vcf.gz.tbi
liftOver_WP019_hg19ToHg38.vcf.gz		liftOver_WP019_hg19ToHg38.vcf.gz
liftOver_WP019_hg19ToHg38.vcf.gz.tbi		liftOver_WP019_hg19ToHg38.vcf.gz.tbi
liftOver_WP058_hg19ToHg38.vcf.gz		liftOver_WP058_hg19ToHg38.vcf.gz
liftOver_WP058_hg19ToHg38.vcf.gz.tbi		liftOver_WP058_hg19ToHg38.vcf.gz.tbi
liftOver_WP068_hg19ToHg38.vcf.gz		liftOver_WP068_hg19ToHg38.vcf.gz
liftOver_WP068_hg19ToHg38.vcf.gz.tbi		liftOver_WP068_hg19ToHg38.vcf.gz.tbi
vep-gc.sh		vep-gc.sh
vep.sh		vep.sh

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lmabrasil-hg38

Workflow

Filtrar variantes somáticas - Workflow

The Human Phenotype Ontology (HPO)

Clonal Hematopoiesis drivers

vep.sh - script

output - .vep.filter.tsv

Cancer Genome Interpreter

Usando CGI via API Rest no Google Colab

Gerando Token no seu usuário CGI

Enviando um Job - job_id: be69dc21d218f22e5f7e

Visualizando os identificadores

Acessando informações do Job

Download dos Resultados (file.zip)

Descompactando o arquivo `file.zip`

Resultado: `alterations.tsv`

Resultado: `biomarkers.tsv`

Deletando o Job do CGI

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renatopuga/lmabrasil-hg38

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Repository files navigation

lmabrasil-hg38

Workflow

Filtrar variantes somáticas - Workflow

The Human Phenotype Ontology (HPO)

Clonal Hematopoiesis drivers

vep.sh - script

output - .vep.filter.tsv

Cancer Genome Interpreter

Usando CGI via API Rest no Google Colab

Gerando Token no seu usuário CGI

Enviando um Job - job_id: be69dc21d218f22e5f7e

Visualizando os identificadores

Acessando informações do Job

Download dos Resultados (file.zip)

Descompactando o arquivo file.zip

Resultado: alterations.tsv

Resultado: biomarkers.tsv

Deletando o Job do CGI

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Descompactando o arquivo `file.zip`

Resultado: `alterations.tsv`

Resultado: `biomarkers.tsv`