SnpEff

SnpEff

test.chr22.vcf

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|