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