BCFTools query regex or boolean expression
Hello,
I would like to extract only some columns from my vcf files like this:
bcftools query --format '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%HF\n' {my_files}.vcf > {out}.txt
My problem is for some vcf outputs (different variant calling tools) I have column named HF for others AF, is it possible to use regex or boolean to extract that columns using only one command line?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Variant Calling Issue
written by Nai •
-
bcftools select sites with multiple combinations of FILTER column
written by User000
-
Combine VCF files
written by Sowmya Pulapet •
-
Extract AD thatt ' support the ALTERNATIVE ALLELE ' from VCF file
written by Maryem •
-
Merge two files with multiple columns by 4 common columns
written by User000
-
Filter VCF FMT DP and Crosscheck Two Samples
written by JellyFrog •
-
Extract the DP and AD from VCF file along with the chromosome postion and alteration
written by manojkumarbioinfo
-
Extract columns from VCF file using bcftools preserving all the header info
written by nikitavlassenko
-
BCFTools Query: Avoid grouping Alt Alleles
written by jon.klonowski
-
Extraction of SNPs from the 1000G vcf file for a set of regions
written by SGMS
no
so I have to launch the same command line twice changing the HF to AF, right?
you can print both tags with
bcftools query --allow-undef-tags --format ...this prints me only
.and notAForHFvaluesExample input and expected output would help others to understand the issue.