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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.
'''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 ==
== Basic Usage Example ==
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 chrom1-CHB.vcf -g genelist.txt -o annotated-chrom1-CHB.vcf
== Command Line Options ==
== 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
-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 ==
== 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
