interspecies conservation scores add_scores $input1 ${input1.metadata.dbkey} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${GALAXY_DATA_INDEX_DIR}/add_scores.loc $out_file1 add_scores

.. class:: warningmark This currently works only for build hg18. ----- **Dataset formats** The input can be any interval_ format dataset. The output is also in interval format. (`Dataset missing?`_) .. _interval: ./static/formatHelp.html#interval .. _Dataset missing?: ./static/formatHelp.html ----- **What it does** This tool adds a column that measures interspecies conservation at each SNP position, using conservation scores for primates pre-computed by the phyloP program. PhyloP performs an exact P-value computation under a continuous Markov substitution model. The chromosome and start position are used to look up the scores, so if a larger interval is in the input, only the score for the first nucleotide is returned. ----- **Example** - input file, with SNPs:: chr22 16440426 14440427 C/T chr22 15494851 14494852 A/G chr22 14494911 14494912 A/T chr22 14550435 14550436 A/G chr22 14611956 14611957 G/T chr22 14612076 14612077 A/G chr22 14668537 14668538 C chr22 14668703 14668704 A/T chr22 14668775 14668776 G chr22 14680074 14680075 A/T etc. - output file, showing conservation scores for primates:: chr22 16440426 14440427 C/T 0.509 chr22 15494851 14494852 A/G 0.427 chr22 14494911 14494912 A/T NA chr22 14550435 14550436 A/G NA chr22 14611956 14611957 G/T -2.142 chr22 14612076 14612077 A/G 0.369 chr22 14668537 14668538 C 0.419 chr22 14668703 14668704 A/T -1.462 chr22 14668775 14668776 G 0.470 chr22 14680074 14680075 A/T 0.303 etc. "NA" means that the phyloP score was not available. ----- **Reference** Siepel A, Pollard KS, Haussler D. (2006) New methods for detecting lineage-specific selection. In Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205.