Difference between revisions of "VcfCodingSnps"

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Here is an example of how <code>vcfCodingSnps</code> works:  
 
Here is an example of how <code>vcfCodingSnps</code> works:  
  
   vcfCodingSnps -s chrom1-CHB.vcf -g genelist.txt -o annotated-chrom1-CHB.vcf
+
   vcfCodingSnps -s chrom22-CHB.vcf -g genelist.txt -o annotated-chrom22-CHB.vcf
  
 
== Command Line Options  ==
 
== Command Line Options  ==
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   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      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
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   ... ...
  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
 

Revision as of 17:19, 12 December 2009

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

Example headlines of input VCF 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
  ... ...