From fc9efb22f5c76cc897725661c1f4e1ab653072de Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Thu, 29 Sep 2022 10:57:08 -0700 Subject: [PATCH] Add CHROM, POS, REF to variant annotations file --- vcf/README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/vcf/README.md b/vcf/README.md index ebc5f3f..6e8177d 100644 --- a/vcf/README.md +++ b/vcf/README.md @@ -25,7 +25,8 @@ Using the ANN section of the INFO column... Create a file and append to it from a bcftools query: + ``` -echo "ID\tAllele\tAnnotation\tAnnotation_Impact\tGene_Name\tGene_ID\tFeature_Type\tFeature_ID\tTranscript_BioType" > variant_annotaions.tsv -bcftools query -f "%ID|%ANN \n" sorghum.filtered.season4.season6.annotated.vcf.gz | cut -d'|' -f 1,2,3,4,5,6,7,8,9 | tr '|' '\t' >> variant_annotaions.tsv +echo "CHROM\tPOS\tID\tREF\tAllele\tAnnotation\tAnnotation_Impact\tGene_Name\tGene_ID\tFeature_Type\tFeature_ID\tTranscript_BioType" > variant_annotaions.tsv +bcftools query -f "%CHROM|%POS|%ID|%REF|%ANN \n" sorghum.filtered.season4.season6.annotated.vcf.gz | cut -d'|' -f 1,2,3,4,5,6,7,8,9 | tr '|' '\t' >> variant_annotaions.tsv ```