-
Notifications
You must be signed in to change notification settings - Fork 6
/
Copy pathblog_spotlight_variants_snpeff.vcf
14 lines (14 loc) · 4.24 KB
/
blog_spotlight_variants_snpeff.vcf
1
2
3
4
5
6
7
8
9
10
11
12
13
14
##fileformat=VCFv4.1
##fileDate=2014/06/17
##source=Manual_Curation_By_Andrew_Jesaitis
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##SnpEffVersion="3.6a (build 2014-04-24), by Pablo Cingolani"
##SnpEffCmd="SnpEff GRCh37.75 -hgvs /Users/andrewjesaitis/Projects/cftr-variant-classification-analysis/variant_subset.vcf "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype_Number [ | ERRORS | WARNINGS ] )' ">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
7 117120154 . A AT . . EFF=FRAME_SHIFT(HIGH||agg/Tagg|p.Arg3X/c.7*>+T|1419|CFTR|protein_coding|CODING|ENST00000454343|1|1),FRAME_SHIFT(HIGH||agg/Tagg|p.Arg3X/c.7*>+T|1437|CFTR|protein_coding|CODING|ENST00000426809|1|1|WARNING_TRANSCRIPT_INCOMPLETE),FRAME_SHIFT(HIGH||agg/Tagg|p.Arg3X/c.7*>+T|1480|CFTR|protein_coding|CODING|ENST00000003084|1|1),INTRON(MODIFIER|||c.-191+407*>+T|35|CFTR|protein_coding|CODING|ENST00000446805|2|1|WARNING_TRANSCRIPT_INCOMPLETE),INTRON(MODIFIER|||n.166+4293*>+T||CFTR|processed_transcript|CODING|ENST00000546407|2|1),STOP_GAINED(HIGH||agg/Tagg|p.Arg3*/c.7*>+T|1419|CFTR|protein_coding|CODING|ENST00000454343|1|1),STOP_GAINED(HIGH||agg/Tagg|p.Arg3*/c.7*>+T|1437|CFTR|protein_coding|CODING|ENST00000426809|1|1|WARNING_TRANSCRIPT_INCOMPLETE),STOP_GAINED(HIGH||agg/Tagg|p.Arg3*/c.7*>+T|1480|CFTR|protein_coding|CODING|ENST00000003084|1|1) GT 0/1
7 117105835 . TTTT T . . EFF=EXON(MODIFIER|||||CFTR|processed_transcript|CODING|ENST00000546407|1|1),INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER||2|||CFTR|processed_transcript|CODING|ENST00000546407||1) GT 0/1
7 117307159 . TT T . . EFF=DOWNSTREAM(MODIFIER||35||1437|CFTR|protein_coding|CODING|ENST00000426809||1|WARNING_TRANSCRIPT_INCOMPLETE),FRAME_SHIFT(HIGH||-/-|p.X1420X/c.4258*>-T|1419|CFTR|protein_coding|CODING|ENST00000454343|26|1),FRAME_SHIFT(HIGH||-/-|p.X1481X/c.4441*>-T|1480|CFTR|protein_coding|CODING|ENST00000003084|27|1),INTRON(MODIFIER|||c.366+1542*>-T|155|CFTR|protein_coding|CODING|ENST00000600166|3|1|WARNING_TRANSCRIPT_NO_START_CODON) GT 0/1
7 117119513 . C CA . . EFF=INTRON(MODIFIER|||c.-423-2*>+A|35|CFTR|protein_coding|CODING|ENST00000446805|1|1|WARNING_TRANSCRIPT_INCOMPLETE),INTRON(MODIFIER|||n.166+3652*>+A||CFTR|processed_transcript|CODING|ENST00000546407|2|1),SPLICE_SITE_ACCEPTOR(HIGH||||35|CFTR|protein_coding|CODING|ENST00000446805|2|1|WARNING_TRANSCRIPT_INCOMPLETE),UPSTREAM(MODIFIER||503||1419|CFTR|protein_coding|CODING|ENST00000454343||1),UPSTREAM(MODIFIER||503||1480|CFTR|protein_coding|CODING|ENST00000003084||1),UPSTREAM(MODIFIER||635||1437|CFTR|protein_coding|CODING|ENST00000426809||1|WARNING_TRANSCRIPT_INCOMPLETE) GT 0/1
7 117144417 . G GATG . . EFF=DOWNSTREAM(MODIFIER||56|||CFTR|processed_transcript|CODING|ENST00000546407||1),INTRON(MODIFIER|||c.-80+1*>+ATG|35|CFTR|protein_coding|CODING|ENST00000446805|3|1|WARNING_TRANSCRIPT_INCOMPLETE),INTRON(MODIFIER|||c.164+1*>+ATG|1419|CFTR|protein_coding|CODING|ENST00000454343|2|1),INTRON(MODIFIER|||c.164+1*>+ATG|1437|CFTR|protein_coding|CODING|ENST00000426809|2|1|WARNING_TRANSCRIPT_INCOMPLETE),INTRON(MODIFIER|||c.164+1*>+ATG|1480|CFTR|protein_coding|CODING|ENST00000003084|2|1),SPLICE_SITE_DONOR(HIGH||||1419|CFTR|protein_coding|CODING|ENST00000454343|2|1),SPLICE_SITE_DONOR(HIGH||||1437|CFTR|protein_coding|CODING|ENST00000426809|2|1|WARNING_TRANSCRIPT_INCOMPLETE),SPLICE_SITE_DONOR(HIGH||||1480|CFTR|protein_coding|CODING|ENST00000003084|2|1),SPLICE_SITE_DONOR(HIGH||||35|CFTR|protein_coding|CODING|ENST00000446805|3|1|WARNING_TRANSCRIPT_INCOMPLETE) GT 0/1
7 117307123 . AGAG A . . EFF=CODON_DELETION(MODERATE||gag/-|p.Glu1408X/c.4222*>-GAG|1419|CFTR|protein_coding|CODING|ENST00000454343|26|1),CODON_DELETION(MODERATE||gag/-|p.Glu1469X/c.4405*>-GAG|1480|CFTR|protein_coding|CODING|ENST00000003084|27|1),DOWNSTREAM(MODIFIER||0||1437|CFTR|protein_coding|CODING|ENST00000426809||1|WARNING_TRANSCRIPT_INCOMPLETE),FRAME_SHIFT(HIGH||-/-|p.X1439X/c.4315*>-GAG|1437|CFTR|protein_coding|CODING|ENST00000426809|26|1|WARNING_TRANSCRIPT_INCOMPLETE),INTRON(MODIFIER|||c.366+1506*>-GAG|155|CFTR|protein_coding|CODING|ENST00000600166|3|1|WARNING_TRANSCRIPT_NO_START_CODON) GT 0/1