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'''vcfCodingSnps'''[http://www.sph.umich.edu/csg/liyanmin/vcfCodingSnps/index.shtml] 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. The tool is currently under development by Yanming Li, a doctoral student at the University of Michigan Center for Statistical Genetics. For any issues with the program, please contact [mailto:liyanmin@umich.edu Yanming]. A detailed tutorial and download page can be found at [http://www.sph.umich.edu/csg/liyanmin/vcfCodingSnps/index.shtml]
'''vcfCodingSnps'''[http://csg.sph.umich.edu//liyanmin/vcfCodingSnps/index.shtml] 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. The tool is currently under development by Yanming Li, a doctoral student at the University of Michigan Center for Statistical Genetics. For any issues with the program, please contact [mailto:liyanmin@umich.edu Yanming]. A detailed tutorial and download page can be found at [http://csg.sph.umich.edu//liyanmin/vcfCodingSnps/index.shtml]
== Basic Usage Example ==
== Basic Usage Example ==
--ns parameter user defined number of kbps for the range of upstream or downstream of a gene, by default will be set t0 5
--ns parameter user defined number of kbps for the range of upstream or downstream of a gene, by default will be set t0 5
== Input File Infomation ==
== Library Compiling Guideline ==
To Compile the source code, please first re-compile the .c functions in the library folder on your local machine:
1. Get into folder "libcsg". Type syntax "gcc -c -O2 *.cpp -D_FILE_OFFSET_BITS=32" to re-compile the c files in the library if use a 32-bit local machine
(Type "gcc -c -O2 *.cpp -D_FILE_OFFSET_BITS=64" to re-compile the .c files in the library if use a 64-bit local machine)
2. In the same folder, type "ar -rc libcsg.a *.o"
3. Go to the root folder, type "make clean" and "make". (Don't need to change anything in Makefile in this step)
== Input File Information ==
1. Example headlines of input VCF-format SNP file:
1. Example headlines of input VCF-format SNP file:
... ...
... ...
2. Input gene file should be a plain text file generated by [http://genome.ucsc.edu/ ucsc genome browser]. A sample pathway of generating an input gene file is
2. The gene list and the reference genome that user provided can be of various gene tracks and assemblies. The latest version takes gene list tracks such as UCSC known genes, RefSeq genes, Genecode genes, CCDS genes and Emsembl genes, and the assembly of the gene list and the reference genome can be of either hg16, hg17, hg18 or hg19. One can explore UCSC genome browser for a better understanding of different tracks and assemblies. By default vcfColdingSnps uses a hg18 UCSC known gene list and the hg18 reference genome. It also provides versions of other tracks and assemblies at the user's conveinience so that they don't need to download those themselves. Input gene file should be a plain text file generated by [http://genome.ucsc.edu/ ucsc genome browser]. A sample pathway of generating an input gene file is
Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file
Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file
1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 10 fields are required and must be of the same order as shown below:
1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 11 tab delimited fields are required and must be of the same order as shown below:
string name; "Name of gene"
string name; "Name of gene"
string chrom; "Chromosome name"
string chrom; "Chromosome name"
uint[exonCount] exonStarts; "Exon start positions"
uint[exonCount] exonStarts; "Exon start positions"
uint[exonCount] exonEnds; "Exon end positions"
uint[exonCount] exonEnds; "Exon end positions"
2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other reasons, the exonframe might not
string symbol; "Standard gene symbol"
match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is not a multiple of three". While we will use the usual mod 3 method for counting codons.
Note: the 11th field is a mandatory field for running vcfCodingSnps. In the genelists provided with the package, this field gives the standard gene symbols such as "APOE", "LDL-R" etc.
If a genelist downloaded by you own that does not contain such a field, you can simply make the 11th field equal to the first field which is the gene name in a specific track by a syntax like
awk `{FS="\t"; print $0"\t"$1 }` yourGenelist > yourNewGenelist
2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other
reasons, the exonframe might not match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is
not a multiple of three". While we will use the usual mod 3 method for counting codons.
3. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables].
3. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables].
4. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570).
4. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570).
8 151936 . a g 32 . depth=105;duples=hets;mac=2;tdt=0/2;5'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=RPL23A_20_869(uc010lrb.1)[-] GT:GQ:GD 0/1:42:44 0/1:23:47 0/0:39:14
8 151936 . a g 32 . depth=105;duples=hets;mac=2;tdt=0/2;5'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=RPL23A_20_869(uc010lrb.1)[-] GT:GQ:GD 0/1:42:44 0/1:23:47 0/0:39:14
8 152578 . c t 87 . depth=108;5'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=RPL23A_20_869(uc010lrb.1)[-] GT:GQ:GD 1/1:95:31 1/1:89:30 1/1:100:47
8 152578 . c t 87 . depth=108;5'UTR=RPL23A_20_869(uc010lra.1)[-];5'UTR=RPL23A_20_869(uc003woq.2)[-];5'UTR=RPL23A_20_869(uc010lrb.1)[-] GT:GQ:GD 1/1:95:31 1/1:89:30 1/1:100:47
Output log file headlines:
##chr pos ref alt ucsc_name genestrend genestart geneend ref_codon ref_AA alt_codon alt_AA codon_start codon_end genesymbol codonCount type
chr2 214811129 T c uc010fuz.1 + 213857360 214814327 CTA Leu CCA Pro 214811128 214811130 SPAG16 433 NON_SYNONYMOUS_CODING
chr2 214811129 T c uc002veq.1 + 213857360 214983470 . . . . . . SPAG16 . INTRONIC
chr2 214811129 T c uc002ver.1 + 213857360 214983470 . . . . . . SPAG16 . INTRONIC
chr2 214811174 T a uc010fuz.1 + 213857360 214814327 . . . . . . SPAG16 . 3'UTR
chr2 214811174 T a uc002veq.1 + 213857360 214983470 . . . . . . SPAG16 . INTRONIC
