SnpEff

最后发布时间 : 2023-03-31 17:30:14 浏览量 :

test.chr22.vcf

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
22	17071756	.	T	C	.	.	.
22	17072035	.	C	T	.	.	.
22	17072258	.	C	A	.	.	.
22	17072674	.	G	A	.	.	.
22	17072747	.	T	C	.	.	.
22	17072781	.	C	T	.	.	.
22	17073043	.	C	T	.	.	.
22	17073066	.	A	G	.	.	.
22	17073119	.	C	T	.	.	.

java -Xmx8g -jar ../snpEff.jar GRCh37.75 ../examples/test.chr22.vcf -nodownload  > test.chr22.ann.vcf

snpEff_summary.html

snpEff_genes.txt

# The following table is formatted as tab separated values.
#GeneName	GeneId	TranscriptId	BioType	variants_impact_HIGH	variants_impact_LOW	variants_impact_MODERATE	variants_impact_MODIFIER	variants_effect_3_prime_UTR_variant	variants_effect_5_prime_UTR_premature_start_codon_gain_variant	variants_effect_5_prime_UTR_variant	variants_effect_conservative_inframe_deletion	variants_effect_conservative_inframe_insertion	variants_effect_disruptive_inframe_deletion	variants_effect_disruptive_inframe_insertion	variants_effect_downstream_gene_variant	variants_effect_frameshift_variant	variants_effect_intron_variant	variants_effect_missense_variant	variants_effect_non_coding_transcript_exon_variant	variants_effect_splice_acceptor_variant	variants_effect_splice_donor_variant	variants_effect_splice_region_variant	variants_effect_start_lost	variants_effect_stop_gained	variants_effect_stop_lost	variants_effect_stop_retained_variant	variants_effect_synonymous_variant	variants_effect_upstream_gene_variant
A4GALT	ENSG00000128274	ENST00000249005	protein_coding	1	10	9	3	2	1	1	0	0	0	0	0	1	0	9	0	0	0	0	0	0	0	0	9	0
A4GALT	ENSG00000128274	ENST00000381278	protein_coding	1	10	9	3	2	1	1	0	0	0	0	0	1	0	9	0	0	0	0	0	0	0	0	9	0
A4GALT	ENSG00000128274	ENST00000401850	protein_coding	1	10	9	3	2	1	1	0	0	0	0	0	1	0	9	0	0	0	0	0	0	0	0	9	0
A4GALT	ENSG00000128274	ENST00000465765	processed_transcript	0	0	0	22	0	0	0	0	0	0	0	22	0	0	0	0	0	0	0	0	0	0	0	0	0
A4GALT	ENSG00000128274	ENST00000483026	processed_transcript	0	0	0	22	0	0	0	0	0	0	0	21	0	0	0	1	0	0	0	0	0	0	0	0	0
AC000029.1	ENSG00000221069	ENST00000408142	miRNA	0	0	0	16	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	4
AC000036.4	ENSG00000225929	ENST00000449652	antisense	0	0	0	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16
AC000068.10	ENSG00000273212	ENST00000608816	antisense	0	0	0	9	0	0	0	0	0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	5

test.chr22.ann.vcf

##SnpEffVersion="5.1d (build 2022-04-19 15:49), by Pablo Cingolani"
##SnpEffCmd="SnpEff  GRCh37.75 ../examples/test.chr22.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
22	17071756	.	T	C	.	.	ANN=C\|3_prime_UTR_variant\|MODIFIER\|CCT8L2\|ENSG00000198445\|transcript\|ENST00000359963\|protein_coding\|1/1\|c.11A>G\|\|\|\|\|11\|,C\|downstream_gene_variant\|MODIFIER\|FABP5P11\|ENSG00000240122\|transcript\|ENST00000430910\|processed_pseudogene\|\|n.4223A>G\|\|\|\|\|4223\|
22	17072035	.	C	T	.	.	ANN=T\|missense_variant\|MODERATE\|CCT8L2\|ENSG00000198445\|transcript\|ENST00000359963\|protein_coding\|1/1\|c.1406G>A\|p.Gly469Glu\|1666/2034\|1406/1674\|469/557\|\|,T\|downstream_gene_variant\|MODIFIER\|FABP5P11\|ENSG00000240122\|transcript\|ENST00000430910\|processed_pseudogene\|\|n.*3944G>A\|\|\|\|\|3944\|
22	17072258	.	C	A	.	.	ANN=A\|missense_variant\|MODERATE\|CCT8L2\|ENSG00000198445\|transcript\|ENST00000359963\|protein_coding\|1/1\|c.1183G>T\|p.Gly395Cys\|1443/2034\|1183/1674\|395/557\|\|,A\|downstream_gene_variant\|MODIFIER\|FABP5P11\|ENSG00000240122\|transcript\|ENST00000430910\|processed_pseudogene\|\|n.*3721G>T\|\|\|\|\|3721\|
22	17072674	.	G	A	.	.	ANN=A\|missense_variant\|MODERATE\|CCT8L2\|ENSG00000198445\|transcript\|ENST00000359963\|protein_coding\|1/1\|c.767C>T\|p.Pro256Leu\|1027/2034\|767/1674\|256/557\|\|,A\|downstream_gene_variant\|MODIFIER\|FABP5P11\|ENSG00000240122\|transcript\|ENST00000430910\|processed_pseudogene\|\|n.*3305C>T\|\|\|\|\|3305\|
22	17072747	.	T	C	.	.	ANN=C\|missense_variant\|MODERATE\|CCT8L2\|ENSG00000198445\|transcript\|ENST00000359963\|protein_coding\|1/1\|c.694A>G\|p.Met232Val\|954/2034\|694/1674\|232/557\|\|,C\|downstream_gene_variant\|MODIFIER\|FABP5P11\|ENSG00000240122\|transcript\|ENST00000430910\|processed_pseudogene\|\|n.*3232A>G\|\|\|\|\|3232\|
22	17072781	.	C	T	.	.	ANN=T\|synonymous_variant\|LOW\|CCT8L2\|ENSG00000198445\|transcript\|ENST00000359963\|protein_coding\|1/1\|c.660G>A\|p.Pro220Pro\|920/2034\|660/1674\|220/557\|\|,T\|downstream_gene_variant\|MODIFIER\|FABP5P11\|ENSG00000240122\|transcript\|ENST00000430910\|processed_pseudogene\|\|n.*3198G>A\|\|\|\|\|3198\|
22	17073043	.	C	T	.	.	ANN=T\|missense_variant\|MODERATE\|CCT8L2\|ENSG00000198445\|transcript\|ENST00000359963\|protein_coding\|1/1\|c.398G>A\|p.Arg133Gln\|658/2034\|398/1674\|133/557\|\|,T\|downstream_gene_variant\|MODIFIER\|FABP5P11\|ENSG00000240122\|transcript\|ENST00000430910\|processed_pseudogene\|\|n.*2936G>A\|\|\|\|\|2936\|

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