Skip to main content

Table 1 Reduction in number of variants to validate with Sanger sequencing for the NS and CAKUT cohorts

From: tarSVM: Improving the accuracy of variant calls derived from microfluidic PCR-based targeted next generation sequencing using a support vector machine

Cohort

Variant quality filter

Total variants

Total variants passing filter

Eligible variants

Pathogenicity filter

NS Cohort

Default

2250

1263

481

156

NS Cohort

tarSVM

2250

1093

408

121

CAKUT Cohort

Default

8812

3300

1564

639

CAKUT Cohort

tarSVM

8812

2347

1135

432

  1. The first column describes the cohort for which the row corresponds. The second column identifies the variant quality filter applied to the dataset. The total variants column refers to the total variants that were called by GATK. The next column shows the number of variants passing a particular variant quality filter for a specific cohort. Eligible variants referrers to all missense and loss of function variants considered for the analysis, excluding frame shift mutations that are considered in the pathogenicity filter. The final column for the pathogenicity filter column displays the number of variants passing having an allele frequency of less than 1 % across all population in the Exome Variant Server, and the variant was either loss of function or predicted to be deleterious by two of MutationTaster, PolyPhen2, and SIFT