for (final Genotype gt : ctx.getGenotypes()) {
final GenotypeBuilder gtBuilder = new GenotypeBuilder(gt);
final List<String> filters = gtFilterStrings.get(gt.getSampleName());
if (filters == null || filters.isEmpty()) {
gtBuilder.filter(PASS_FILTER);
}
else {
gtBuilder.filters(filters);
}
newGenotypes.add(gtBuilder.make());