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VcfCodingSnps

1,491 bytes added, 14:27, 14 May 2010
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Some possible annotating results for a single SNP with the meanings of their output format are listed below:
5'UTR=A26C2[-] means the SNP is in the 5'UTR region of gene A26C2 with a minus strand. INTRONIC=POTEG[-] means the SNP is in the intronic region of gene POTEG with a minus strand.
SYNONYMOUS_CODING=BARD1(uc002veu.2):His506His[-] means the SNP is synonymous coding at the 506th codon in gene BARD1 with a minus strand and it keeps amino-acid His unchanged.
NON_SYNONYMOUS_CODING=BARD1(uc002veu.2):Arg658Cys[-] means the SNP is non_synonymous coding at the 658th codon in gene BARD1 (ucsc gene name uc002veu.2)with a minus strand and it changes amino-acid from Arg to Cys.
SPLICE_SITE=FARP2(uc002wbi.1)[+] means the SNP is in the SPLICE_SITE (5 bp within exon start or end positions in the coding region) of gene FARP2 (ucsc gene name uc002wbi.1) with a plus strand.
STOP_GAINED=C2orf83(uc002vph.1):Trp141stop[-] means the SNP is the 141th codon in gene MAPK12 (ucsc gene name uc002vph.1) with a minus strand and it changes amino-acid Trp to a stop codon.
STOP_LOST=OR2M3(uc001ieb.1):stop313Arg[+] means the SNP is the 313th codon in gene OR2M3 (ucsc gene name uc001ieb.1) with a plus strand and it changes a stop codon to amino-acid Arg.
The annotating result will be added to the entry "INFO" of the input VCF SNP file and outputted together with other information. If a SNP is annotated differently with respect to different genes (or different isoforms of the same gene), all the annotated results will be added into the entry "INFO". If the SNP is NOT in any gene coding region, then the original "INFO" will be outputted. Here is an example of output VCF file headlines:
##format=VCFv3.2 ##NA12891=../GLF/NA12891.chrom22chrom8.SLX.SRP000032.2009_07.glf ##NA12892=../GLF/NA12892.chrom22chrom8.SLX.SRP000032.2009_07.glf ##NA12878=../merged/NA12878.chrom22chrom8.merged.glf ##minTotalDepth=0 ##maxTotalDepth=1000 ##minMapQuality=40 ##minPosterior=0.9990 ##program=glfTrio ##versionDate=Thu Aug 27 18:23:18 2009 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891 NA12892 NA12878 22 8 146284 . c a 54 . depth=29;duples=hets;mac=2;tdt=0/2 15464609 GT:GQ:GD 1/0:31:12 1/0:32:3 0/0:28:148 146703 . a c g t 100 92 . depth=10941;mac=1;tdt=0/1 GT:GQ:GD 1/1:42:14 0/1:54:9 1/1:24:188 151532 . t c 100 . depth=131;35'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=psiTPTE22RPL23A_20_869(uc010lrb.1)[+-] GT:GQ:GD 0/0:8:37 1/0:100:26 1/0:100:44 688 151573 . g t 72 . depth=113;mac=1;tdt=1/1;5'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=RPL23A_20_869(uc010lrb.1)[-] GT:GQ:GD 0/1:48:35 0/0:8139:28 26 10/1:100:3752 22 15464609 8 151638 . a g c 100 . depth=109124;duples=hets;mac=12;tdt=01/2;5'UTR=RPL23A_20_869(uc010lra.1)[-];35'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=psiTPTE22RPL23A_20_869(uc010lrb.1)[+-] GT:GQ:GD 0/1:100:44 55 10/1:81100:28 158 0/1:10087:3711 22 15464609 8 151651 . a c g 100 . depth=109124;duples=hets;mac=12;tdt=01/2;5'UTR=RPL23A_20_869(uc010lra.1)[-];35'UTR=psiTPTE22RPL23A_20_869(uc003woq.2)[+-] ;5'UTR=RPL23A_20_869(uc010lrb.1)[-] GT:GQ:GD 0/1:10087:44 156 0/1:81100:28 156 0/1:10024:3712 22 15464609 8 151763 . t a g 100 . depth=109127;duples=hets;mac=12;tdt=01/2;5'UTR=RPL23A_20_869(uc010lra.1)[-];35'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=psiTPTE22RPL23A_20_869(uc010lrb.1)[+-] GT:GQ:GD 1/0/1:100:44 49 1/10:81100:28 54 1/10:100:3724 22 15482433 8 151936 . a g 38 32 . depth=21105;duples=hets;3mac=2;tdt=0/2;5'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=psiTPTE22RPL23A_20_869(uc010lrb.1)[+-] GT:GQ:GD 10/1:3442:11 44 10/1:1423:3 147 0/10:3539:714 22 15644565 8 152578 . g c t 77 87 . depth=140108;5'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];NON_SYNONYMOUS_CODING5'UTR=XKR3:His15644565AsnRPL23A_20_869(uc010lrb.1)[-] GT:GQ:GD 1/1:95:31 1/1:89:30 1/1:100:4947
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