VcfCodingSnps
vcfCodingSnps is a SNP annotation tool that annotates coding variants in a VCF format input file. It takes a VCF as input and generates an annotated VCF file as output.
Basic Usage Example
Here is an example of how vcfCodingSnps
works:
vcfCodingSnps -s chrom22-CHB.vcf -g genelist.txt -o annotated-chrom22-CHB.vcf
Command Line Options
-s SNP file Specifies the name of the input VCF-format SNP file -g genefile Specifies the name of the input gene file, by default use gene list file in ASCII format generated by UCSC genome browser -o output file Specifies the name of the output VCF-format SNP file
Input File Infomation
1. Example headlines of input VCF-format SNP file:
##format=VCFv3.2 ##NA12891=../depthFilter/filtered.NA12891.chrom22.SLX.maq.SRP000032.2009_07.glf ##NA12892=../depthFilter/filtered.NA12892.chrom22.SLX.maq.SRP000032.2009_07.glf ##NA12878=../merged/NA12878.chrom22.merged.glf ##minTotalDepth=0 ##maxTotalDepth=1000 ##minMapQuality=30 ##minPosterior=0.9990 ##program=glfTrio ##versionDate=Tue Dec 1 00:42:24 2009 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891 NA12892 NA12878 22 14439753 . a t 100 mapQ=0 depth=68;duples=homs;mac=2 GT:GQ:DP 1|1:100:40 0|0:81:28 1|0:84:0 22 14441250 . t c 59 mapQ=0 depth=40 GT:GQ:DP 1|1:56:25 1|1:31:15 1|1:32:0 22 14443154 . t g 45 mapQ=9 depth=92;duples=homs;mac=2 GT:GQ:DP 1|1:49:21 0|0:60:20 1|0:100:51 ... ...
2. Input gene file should be a plain text file generated by ucsc genome browser. A sample pathway of generating an input gene file is
Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► get output gene file 1. A detailed instruction on using the table browser could be found at genome.ucsc.edu/cgi-bin/hgTables. 2. One can specify the regieon to be whole genome or any particular gene position (e.g. chr21:33031597-33041570).
Here is an example of input gene file headlines:
#name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds proteinID alignID uc001aaa.3 chr1 + 11873 14409 11873 11873 3 11873,12612,13220, 12227,12721,14409, uc001aaa.3 uc010nxq.1 chr1 + 11873 14409 12189 13639 3 11873,12594,13402, 12227,12721,14409, B7ZGX9 uc010nxq.1 uc010nxr.1 chr1 + 11873 14409 11873 11873 3 11873,12645,13220, 12227,12697,14409, uc010nxr.1 uc009vis.2 chr1 - 14362 16765 14362 14362 4 14362,14969,15795,16606, 14829,15038,15942,16765, uc009vis.2 uc009vjc.1 chr1 - 16857 17751 16857 16857 2 16857,17232, 17055,17751, uc009vjc.1 uc009vjd.2 chr1 - 15795 18061 15795 15795 5 15795,16606,16857,17232,17605, 15947,16765,17055,17368,18061, uc009vjd.2
Output File
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=GAB4:Ala15826157Ala[-] means that the SNP is synonymous coding at position 15826167 in gene GAB4 with a minus strand and it keeps amino-acid Ala unchaged. NON_SYNONYMOUS_CODING=GAB4:Leu15830952Pro[-] means that the SNP is non_synonymous coding at position 15830925 in gene GAB4 with a minus strand and it changes amino-acid Leu to Pro. 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.
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