diff --git a/doc/source/data_import.rst b/doc/source/data_import.rst index e5505813986b532c1f63af475df4a37082960bd8..08faaee5938a943f2a1d7106c533f3e37b038977 100644 --- a/doc/source/data_import.rst +++ b/doc/source/data_import.rst @@ -106,10 +106,26 @@ Creation of the JASS inittable Once, GWAS summary statistics are harmonized, they are integrated into one file by the using jass command (see detail in command line usage) -``` -jass create-inittable --input-data-path '$GWAS_files_glob_pattern' --init-covariance-path $path_to_covariance_file --regions-map-path $path_to_LD_regions --description-file-path $path_to_gwas_meta_data.csv --init-table-path $path_to_output_inittable +.. code-block:: shell + + jass create-inittable --input-data-path '$GWAS_files_glob_pattern' --init-covariance-path $path_to_covariance_file --regions-map-path $path_to_LD_regions --description-file-path $path_to_gwas_meta_data.csv --init-table-path $path_to_output_inittable + +Add genes and exons annotation to initTable (optional) +------------------------------------------------------ +If you want to avoid a (non-blocking) error in the JASS web interface when performing a local analysis on a region of the genome, +you must add the genes and exons to the InitTable + +To do this, you need to download the file: RefSeq Reference Genome Annotation GRCh37 from the website: https://www.ncbi.nlm.nih.gov/genome/guide/human/ +before unzipping it on your computer and saving it in the JASS_DATA_DIR folder. Then you can run in a terminal the following command: + +.. code-block:: shell + + jass add-gene-annotation --gene-data-path GRCh37_latest_genomic.gff --init-table-path $path_to_initTable.hdf5 --gene-csv-path df_gene.csv --exon-csv-path df_exon.csv -``` +.. warning:: + For this command, it is necessary to specify the full path of initTable.hdf5 even if this file is in the JASS_DATA_DIR folder. You can use the environment variable $JASS_DATA_DIR (Linux) or %JASS_DATA_DIR% (Windows) +The advantage of adding genes and exons in the initTable is to have an additional graph in the web page of the results of the local analysis: +the position of genes and exons in the studied genomic region (see paragraph: **web usage, section B - Analysis by region**) .. bibliography:: reference.bib