amino-acid changes caused by a set of SNPs codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 > $out_file1 cat sort ucsc_tools

.. class:: infomark The build must be defined for the input files and must be the same for both files. Use the pencil icon to add the build to the files if necessary. ----- **Dataset formats** The SNP dataset is in interval_ format, with a column of SNPs as described below. The gene dataset is in BED_ format with 12 columns. The output dataset is also interval. (`Dataset missing?`_) .. _interval: ./static/formatHelp.html#interval .. _BED: ./static/formatHelp.html#bed .. _Dataset missing?: ./static/formatHelp.html ----- **What it does** This tool identifies which SNPs create amino-acid changes in the specified coding regions. The first input file contains the SNPs and must be an interval file. It needs the chromosome, start, and end position as well as the SNP. The SNP can be given using ambiguous-nucleotide symbols or a list of two to four alleles separated by '/'. Any other columns in the first input file will not be used but will be kept for the output. The second input file contains the genes to be used for defining the coding regions. This file must be a BED file with the first 12 columns standard BED columns. The output is the same as the first input file with several columns added: the name field from the line of the gene input file used, the amino acids, the codon number, and the reference nucleotide that changed in the amino acid. The amino acids are listed with the reference amino acid first, then a colon, and then the amino acids for the alleles. If a SNP is not in a coding region or is synonymous then it is not included in the output file. ----- **Example** - first input file, with SNPs:: chr22 15660821 15660822 A/G chr22 15825725 15825726 G/T chr22 15827035 15827036 G chr22 15827135 15827136 C/G chr22 15830928 15830929 A/G chr22 15830951 15830952 G chr22 15830955 15830956 C/T chr22 15848885 15848886 C/T chr22 15849048 15849049 A/C chr22 15919711 15919712 A/G etc. or, indicating polymorphisms using ambiguous-nucleotide symbols:: chr22 15660821 15660822 R chr22 15825725 15825726 K chr22 15827035 15827036 G chr22 15827135 15827136 S chr22 15830928 15830929 R chr22 15830951 15830952 G chr22 15830955 15830956 Y chr22 15848885 15848886 Y chr22 15849048 15849049 M chr22 15919711 15919712 R etc. - second input file, with UCSC annotations for human genes:: chr22 15688363 15690225 uc010gqr.1 0 + 15688363 15688363 0 2 587,794, 0,1068, chr22 15822826 15869112 uc002zlw.1 0 - 15823622 15869004 0 10 940,105,97,91,265,86,251,208,304,282, 0,1788,2829,3241,4163,6361,8006,26023,29936,46004, chr22 15826991 15869112 uc010gqs.1 0 - 15829218 15869004 0 5 1380,86,157,304,282, 0,2196,21858,25771,41839, chr22 15897459 15919682 uc002zlx.1 0 + 15897459 15897459 0 4 775,128,103,1720, 0,8303,10754,20503, chr22 15945848 15971389 uc002zly.1 0 + 15945981 15970710 0 13 271,25,147,113,127,48,164,84,85,12,102,42,2193, 0,12103,12838,13816,15396,17037,17180,18535,19767,20632,20894,22768,23348, etc. - output file, showing non-synonymous substitutions in coding regions:: chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 T chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 C chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 C chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 C chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 A chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 T chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 G chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 G chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 C etc.