Genomic data integration and user-defined sample-set extraction for population variant analysis

BMC Bioinformatics

Table 1 Comparison of the features of bioinformatics tools providing aggregated statistics over the variants of a population

	gnomAD	Ensembl	PGG.SNV	EVS	IGIB group
(i) Filters on population by metadata	Limited^a	–	–	–	–
(ii) Filters on population by region data	–	–	–	–	–
(iii) Gene annotations	\(\checkmark\)	\(\checkmark\)	\(\checkmark\)	\(\checkmark\)	\(\checkmark\)
(iv) Quality metrics	\(\checkmark\)	-	\(\checkmark\)	\(\checkmark\)	–
(v) Statistics grouped on metadata	Limited^b	Limited^c	Limited^c	Limited^c	Limited^c
(vi) API	–	\(\checkmark\)	–	–	–

The evaluation concerns (i) the availability of filters on metadata attributes to select a subset of the donors from the dataset, i.e., the population of interest; (ii) the availability of filters to consider only the donors showing particular genomic features (either precise variants or mutated genome regions) distinct from the genomic variant studied in the population; (iii) the possibility to look at the gene annotations and (iv) sequencing quality metrics information concerning a genomic region or variant; (v) the possibility to group the result statistics on the metadata; (vi) the availability of an API
^aAnalysis results are available considering all the donors or one of the seven predefined partitions. On top of the chosen partition, it is also possible to further limit the population to an ethnic group, country (when available), or gender type
^bThe statistics about the variant frequency can be grouped by ethnicity, gender, or geographical origin, if the population has not been already filtered on these attributes. In addition, it is possible to know the age distribution of the donors included in the population and of the variant carriers.
^cOnly for the groups identified by the original sequencing project and/or for the geographical origin of the donors

ISSN: 1471-2105