I have successfully extracted the necessary information by using below script; bcftools query -f '%CHROM \t%POS\n' sample1.vcf.gz > sample1.txt
However, I have more than 100 samples in my hand, therefore, I wanted to automate this process with the below script; bcftools query -f '%CHROM \t%POS\n' *.vcf.gz > *.txt
Then I got an error saying failed to read from sample2.vcf: not compressed with bgzip. Thus, I made bgzip files using a following script, htslib/bgzip -c sample1.vcf > sample1.vcf.gz, and redid the abovementioned script. It looked OK, there were no errors showed up, but I only got one txt file in the end, not for all vcf files.
- My question is how I can fix this problems or how I can write a proper script to automate this process?
- Additional question related to this is, how researchers/engineers in the world automate these labor works? When I compressed vcf files by bgzip to make vcf.gz files, I also did one by one manually, which I also would like to automate by running a proper script.