I have vcf.gz file I am trying to merge with bcftools . when I am using the command line it works
bcftools index -f file 1
bcftools index -f file 2
bcftools merge file1 file2 > out.vcf
I get the following error when I call the commands from R or Python:
the file is not BGZF compressed
The files are gzip-compressed variants. Why it's working only through the command line?