lmabrasil-hg38

Versão Reduzida no Google Colab:

Workflow

Filtrar variantes somáticas - Workflow

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1. Clonar repositório renatopuga/lmabrasil-hg38
2. Instalar bcftools +split-vep
3. Instalar udocker
4. 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)

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

• DP>=20 AND AF>=0.1

6. Resultado: *.vep.filter.tsv

The Human Phenotype Ontology (HPO)

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

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

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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	AGCAGAGGCTTAAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGA...	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