Filter and Merge Result Databases

Filter Result Databases

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.

Syntax

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

Example

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.

Merge Result Databases

OpenCRAVAT result database files which were produced with exactly the same set of annotators can be merged with the following command.

Syntax

oc util mergesqlite INPUT [INPUT]... -o OUTPUT

INPUT	Path to an OpenCRAVAT result database file
OUTPUT	Path to a merged OpenCRAVAT result database file

Example

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.