Filtering VCF variants based on txt file with variants CHROM, POS and ID
Hello everyone!
Let's say I have a vcf file (version 4.2). Then, I have a list of variants that I want to exclude from my VCF file. This list is a TXT file containing 3 columns: chromosome, position and ID (dbsnp) where available.
For example, lets say I have the data from this database:
http://srv00.recas.ba.infn.it/atlas/download.html
Then I select the three columns of chromosome name, position and ID for dbsnp.
Is there anyway to remove these variants from my VCF files?
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Ram
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avelarbio46 •
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avelarbio46 •
1 answer
You only need CHR and POS from the file. Use bcftools view -T ^file.txt. See: https://samtools.github.io/bcftools/bcftools.html#view
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