VcfCodingSnps: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
'''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 | == 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:
- 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
