From e660954c0e3f441dc5b8c6ccfaa79caeea5079d5 Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Tue, 23 Jan 2024 09:22:12 -0600 Subject: [PATCH] put the input in the correct place --- pggb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pggb b/pggb index edb0f93..ec6c9c7 100755 --- a/pggb +++ b/pggb @@ -669,7 +669,7 @@ if [[ $vcf_spec != false ]]; then #TODO: remove "bcftools annotate" when vcfwave will be bug-free. # The TYPE info sometimes is wrong/missing and there are variants without the ALT allele. - bcftools sort -T "$temp_dir" | bcftools annotate -x INFO/TYPE "$vcf_decomposed_tmp" | awk '$5 != "."' > "$vcf_decomposed" + bcftools sort -T "$temp_dir" "$vcf_decomposed_tmp" | bcftools annotate -x INFO/TYPE | awk '$5 != "."' > "$vcf_decomposed" rm "$vcf_decomposed_tmp" "$vcf".gz bcftools stats "$vcf_decomposed" > "$vcf_decomposed".stats