VcfCodingSnps

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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 chrom1-CHB.vcf -g genelist.txt -o annotated-chrom1-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

An example headlines of input VCF file:

    1. format=VCFv3.2
    2. NA12891=../depthFilter/filtered.NA12891.chrom22.SLX.maq.SRP000032.2009_07.glf
    3. NA12892=../depthFilter/filtered.NA12892.chrom22.SLX.maq.SRP000032.2009_07.glf
    4. NA12878=../merged/NA12878.chrom22.merged.glf
    5. minTotalDepth=0
    6. maxTotalDepth=1000
    7. minMapQuality=30
    8. minPosterior=0.9990
    9. program=glfTrio
    10. versionDate=Tue Dec 1 00:42:24 2009
  1. 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 22 14446720 . c t 52 mapQ=0 depth=81;duples=homs;mac=2 GT:GQ:DP 1|1:23:31 0|0:23:34 1|0:76:16 22 14446721 . a g 49 mapQ=0 depth=82;duples=homs;mac=2 GT:GQ:DP 1|1:21:30 0|0:21:36 1|0:100:16 22 14449771 . g a 78 mapQ=27 depth=68;mac=1;tdt=1/1 GT:GQ:DP 1|0:64:21 0|0:75:36 1|0:28:11