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SPLICE_SITE=NCAPH2[+] means that the SNP is in the SPLICE_SITE (5 bp within exon start or end positions in the coding reegion) of gene MCAPH2 with a plus strand.
SPLICE_SITE=NCAPH2[+] means that the SNP is in the SPLICE_SITE (5 bp within exon start or end positions in the coding reegion) of gene MCAPH2 with a plus strand.
STOP_GAINED=MAPK12:Trp49035685stop[-] means that the SNP is at position 49035685 in gene MAPK12 with a minus strand and it changes amino-acid Trp to a stop codon.
STOP_GAINED=MAPK12:Trp49035685stop[-] means that the SNP is at position 49035685 in gene MAPK12 with a minus strand and it changes amino-acid Trp to a stop codon.
The annotating result will be added to the entry "INFO" of the input VCF file and outputted together with other information in the input VCF SNP file. Here is an example of output VCF file headlines:
##format=VCFv3.2
##NA12891=../GLF/NA12891.chrom22.SLX.SRP000032.2009_07.glf
##NA12892=../GLF/NA12892.chrom22.SLX.SRP000032.2009_07.glf
##NA12878=../merged/NA12878.chrom22.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 15464609 . a g 100 . depth=109;mac=1;tdt=0/1;3'UTR=psiTPTE22[+] GT:GQ:GD 0/1:100:44 1/1:81:28 1/1:100:37
22 15464609 . a g 100 . depth=109;mac=1;tdt=0/1;3'UTR=psiTPTE22[+] GT:GQ:GD 0/1:100:44 1/1:81:28 1/1:100:37
22 15464609 . a g 100 . depth=109;mac=1;tdt=0/1;3'UTR=psiTPTE22[+] GT:GQ:GD 0/1:100:44 1/1:81:28 1/1:100:37
22 15464609 . a g 100 . depth=109;mac=1;tdt=0/1;3'UTR=psiTPTE22[+] GT:GQ:GD 0/1:100:44 1/1:81:28 1/1:100:37
22 15482433 . a g 38 . depth=21;3'UTR=psiTPTE22[+] GT:GQ:GD 1/1:34:11 1/1:14:3 1/1:35:7
22 15644565 . g t 77 . depth=140;NON_SYNONYMOUS_CODING=XKR3:His15644565Asn[-] GT:GQ:GD 1/1:100:49
