Difference between revisions of "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.
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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 ==
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== Basic Usage Example ==
  
Here is an example of how <code>vcfCodingSnps</code> works:
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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 chrom1-CHB.vcf -g genelist.txt -o annotated-chrom1-CHB.vcf
  
== Command Line Options ==
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== Command Line Options ==
  
 
   -s ''SNP file''                    Specifies the name of the input [[VCF]]-format SNP file
 
   -s ''SNP file''                    Specifies the name of the input [[VCF]]-format SNP file
   -g ''genefile''                    Specifies the name of the gene file, by default use gene list file in ASCII format generated by UCSC genome browser  
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   -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
 
   -o ''output file''                Specifies the name of the output VCF-format SNP file
  
== Input file infomation ==
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== Input File Infomation ==
 +
 
 +
An 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
 +
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

Revision as of 17:17, 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 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