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--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
== Library Compiling Guideline ==
== Library Compiling Guideline ==
To Compile the source code, please first re-compile the .c functions in the library folder on your local machine:
To Compile the source code, please first re-compile the .c functions in the library folder on your local machine:
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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
uint[exonCount] exonEnds; "Exon end positions"
uint[exonCount] exonEnds; "Exon end positions"
string symbol; "Standard gene symbol"
string symbol; "Standard gene symbol"
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
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
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
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:
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
##chr pos ref alt ucsc_name genestrend genestart geneend ref_codon ref_AA alt_codon alt_AA codon_start codon_end genesymbol codonCount type
