Filtering

--filtersql can be used to generated filtered output files. This option can be used in ov run and ov report. For example,

ov run input.vcf --filtersql "v.base__chrom='chr1'" -t csv

will generate a CSV format output file of the variants that are filtered by the criterion that the chromosome of the variant is chr1.

The v. in front of base__chrom means the variant table in the result database. g. will mean the gene table, and s the sample table.

base__chrom means base module's chrom column. base module is an abstract column which includes the basic variant information as well as the mapper module. Other column names are used as they are. After a module name and "__" (double underline), a column name follows. Thus, clinvar__sig means cliuvar module's sig column. Thus, generating a VCF format output of the variants filtered with the criterion that the variants are Pathogenic in ClinVar would be

ov report input.vcf --filtersql "clinvar__sig='Pathogenic'" -t vcf

SQL's where command syntax is used. Thus, and and or can be used as well. For example,

ov report input.vcf -a clinvar --filtersql "base__hugo='BRCA1' and clinvar__sig like '%Pathogenic%' -t vcf"

will annotate the input file with the ClinVar module and generate a VCF format output of the variants filtered by two criteria, the gene being BRCA1 and the ClinVar significance has Pathogenic.