by_sample

-- by_sample report

By using the tag --by_sample with the analyse or sort option, you will generate a report that will show for each sample the 5 most probably pathogenic variants.

This obviously requires multi-sample vcf.

Example

Sample_9
Chr	Start	End	Ref	Alt	Allele	ExonicFunc.refGene	Gene.refGene	Probability_Path	Prediction_ACMG_tapes
17	7574017	7574017	C	T	T	missense_variant	TP53	0.9999	Pathogenic
17	7574017	7574017	C	T	T	missense_variant	TP53	0.9999	Pathogenic
13	32953932	32953932	T	A	A	stop_gained	BRCA2	0.9999	Pathogenic
17	7574017	7574017	C	T	T	missense_variant	TP53	0.9999	Pathogenic
14	45606305	45606305	G	A	A	stop_gained	FANCM	0.9998	Pathogenic
Sample_12
Chr	Start	End	Ref	Alt	Allele	ExonicFunc.refGene	Gene.refGene	Probability_Path	Prediction_ACMG_tapes
13	32968863	32968863	C	G	G	stop_gained	BRCA2	1	Pathogenic
17	59793412	59793412	G	A	A	stop_gained	BRIP1	1	Pathogenic
17	7574017	7574017	C	T	T	missense_variant	TP53	0.9999	Pathogenic
17	7574017	7574017	C	T	T	missense_variant	TP53	0.9999	Pathogenic
17	7574017	7574017	C	T	T	missense_variant	TP53	0.9999	Pathogenic