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, 02:25, 13 December 2010
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| uint[exonCount] exonEnds; "Exon end positions" | | uint[exonCount] exonEnds; "Exon end positions" |
| string symbol; "Standard gene symbol" | | string symbol; "Standard gene symbol" |
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| 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 | | 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 |
− | 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 | | 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 |