problem with bcftools syntax

problem with bcftools syntax

1

Hi all!

I am having difficulty with creating a bcftools command. I have a .vcf.gz file downloaded from the 1000G site and a csv file with columns chrom/pos/id/ref/alt. I would like to manipulate the downloaded vcf file so that it uses only the snps I have in my csv file.

To do so I first created a txt file like this:

awk -F';' 'NR > 1 {print $1, $2}' chr.csv > regions.txt

Then I wanted to use bcftools in such a way:

bcftools view -T regions.txt -O z -o filtered_chr.vcf.gz ALL.chr.vcf.gz

But this unfortunately gives me such an error:

[E::bcf_sr_regions_init] Could not parse 1-th line of file
regions.txt, using the columns 1,2[,-1] Failed to read the targets:
regions.txt

What am I doing wrong? Is my bcftools syntax command wrong, or maybe my regions.txt file should be created differentely?

I would really appreciate any help!


bioinformatics


syntax


vcf


bcftools


command

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