OpenCRAVAT jobs produce result database files which are SQLite files. The variants and samples in these result databases can be filtered into new result databases.
oc util filtersqlite INPUT [INPUT]... -o OUTDIR -s SUFFIX -f FILTERPATH --filtersql FILTERSQL --includesample SAMPLE [SAMPLE]... --excludesample SAMPLE [SAMPLE]...
| INPUT | Path to a result database file to filter |
| OUTDIR | Path to a folder where new database files will be created |
| SUFFIX | Suffix for new database files. Default is filtered. For example, if INPUT is example.sqlite and SUFFIX is new, example.new.sqlite will be created with filtered variants and samples. |
| FILTERPATH | Path to a filter JSON file |
| FILTERSQL | SQL-format string of filters (see Filter SQL section) |
| SAMPLE | Sample names to include or exclude |
oc util filtersqlite example.sqlite another_result.sqlite --filtersql '(v.base__so=="MIS" and v.clinvar__sig=="Pathogenic")' --excludesample badsample1 badsample2
example.filtered.sqlite and another_result.filtered.sqlite will be created with the default filtered suffix and with filtered variants which are missense variants
in representative transcripts (MANE transcripts by default) and have Pathogenic ClinVar significance.
Samples badsample1 and badsample2 and variants from them will be excluded.
oc util filtersqlite result.sqlite -f filter.json --suffix new -o ~/filtered_results
result.new.sqlite will be created in ~/filtered_results folder with the filters defined in filter.json file.
OpenCRAVAT result database files which were produced with exactly the same set of annotators can be merged with the following command.
oc util mergesqlite INPUT [INPUT]... -o OUTPUT
| INPUT | Path to an OpenCRAVAT result database file |
| OUTPUT | Path to a merged OpenCRAVAT result database file |
oc util mergesqlite result.sqlite another_result.sqlite -o merged.sqlite
The variants and samples in result.sqlite and another_result.sqlite will be merged and written to merged.sqlite.