From ecf415ef270bdea80f437c7a49b1862f3abe5b66 Mon Sep 17 00:00:00 2001 From: Bohan Ni Date: Tue, 7 Jan 2025 14:20:15 -0500 Subject: [PATCH] fixed typo filter-rareness -> filter-rare --- scripts/executable_scripts/generate_annotations_ABC.sh | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/scripts/executable_scripts/generate_annotations_ABC.sh b/scripts/executable_scripts/generate_annotations_ABC.sh index ae66355..4045831 100755 --- a/scripts/executable_scripts/generate_annotations_ABC.sh +++ b/scripts/executable_scripts/generate_annotations_ABC.sh @@ -144,7 +144,7 @@ if [ "$pipeline" == "population" ]; then --lifted-coord $liftover_bed \ --extract-genotype \ --infer-rareness \ - --filter-rareness \ + --filter-rare \ --filter-ethnicity \ --metadata $metadata \ --genotype-filters $filters \ @@ -158,7 +158,7 @@ if [ "$pipeline" == "population" ]; then --lifted-coord $liftover_bed \ --extract-genotype \ --infer-rareness \ - --no-filter-rareness \ + --no-filter-rare \ --filter-ethnicity \ --metadata $metadata \ --genotype-filters $filters \ @@ -174,7 +174,7 @@ if [ "$pipeline" == "population" ]; then --lifted-coord $liftover_bed \ --extract-genotype \ --infer-rareness \ - --filter-rareness \ + --filter-rare \ --no-filter-ethnicity \ --genotype-filters $filters \ --out-annotsv ${outdir}/intermediates/vep_input.tsv \ @@ -187,7 +187,7 @@ if [ "$pipeline" == "population" ]; then --lifted-coord $liftover_bed \ --extract-genotype \ --infer-rareness \ - --no-filter-rareness \ + --no-filter-rare \ --no-filter-ethnicity \ --genotype-filters $filters \ --out-annotsv ${outdir}/intermediates/vep_input.tsv \ @@ -203,7 +203,7 @@ elif [ "$pipeline" == "smallset" ]; then --vcf $input_vcf \ --extract-genotype \ --no-infer-rareness \ - --no-filter-rareness \ + --no-filter-rare \ --no-filter-ethnicity \ --genotype-filters ${filters} \ --out-annotsv ${outdir}/intermediates/vep_input.tsv \