problem with bcftools syntax
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!
• 37 views
Read more here: Source link