exclude variants based on position in vcf file
I have a list of positions (POS) in a text file I would like to remove from a .vcf file. What is the simplest way to do this? I have tried:
vcftools --vcf cluster_1_private.vcf --exclude remove_poly_1.txt --recode --recode-INFO-all --out cluster_1_fixed
but this doesnt seem to work, but note the text file only contains a list of numbers such as:
3416
14547
55489
56775
66521
91512
Maybe I need to specify the POS somehow?
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goatsrunfaster •
1 answer
Figure it out:
vcftools --vcf cluster_1_private.vcf --exclude-positions remove_poly_1.txt --recode --recode-INFO-all --out cluster_1_fixed
text file needs to be a tab-separated list of chromosome and positions
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goatsrunfaster •
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