Sorry if this has been answered before (though I have not found an appropriate answer already) What is an effective way to extract mutliple chromosomal regions from a vcf.gz file? I see that it can be done for single regions using tabix, but I have a file with several regions in a text file in the format:
chromosome:startposition-endposition eg: 19:47366525-47380539
Perhaps there is a way to refer to a file of regions using tabix, or vcf-tools? If anyone could provide an example command line that would be really helpful.
Thanks in advance!
tabix my.vcf.gz chromosome_name:start_position-end_position -h > out.vcf