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VcfCodingSnps

11 bytes added, 14:31, 14 May 2010
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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 input and output VCF file headlines:   
##format=VCFv3.2
##versionDate=Thu Aug 27 18:23:18 2009
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891 NA12892 NA12878
 
8 146284 . c a 54 . depth=29;duples=hets;mac=2;tdt=0/2 GT:GQ:GD 1/0:31:12 1/0:32:3 0/0:28:14 8 146703 . c t 92 . depth=41;mac=1;tdt=0/1 GT:GQ:GD 1/1:42:14 0/1:54:9 1/1:24:18
8 151532 . t c 100 . depth=131;5'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=RPL23A_20_869(uc010lrb.1)[-] GT:GQ:GD 0/0:8:37 1/0:100:26 1/0:100:68
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