bcftools merge in1.vcf.gz in2.vcf.gz|bcftools filter -e 'GT="./."' > out.vcf If you are interested to find out which variants are in all your vcf files, without merging them than the term you are looking for is intersect. # Extract and write records from A shared by both A and B using exact allele match bcftools isec A.vcf.gz B.vcf.gz -p dir -n ...
Sep 02, 2020 · version development ## Copyright (c) 2020 Giulio Genovese ## ## Version 2020-09-02 ## ## Contact Giulio Genovese
Input devices, like a keyboard, allow us to put raw data in a computer which it processes to produce outputs. Input devices can be manual or automatic.
Jul 22, 2020 · version development ## Copyright (c) 2020 Giulio Genovese ## ## Version 2020-07-22 ## ## Contact Giulio Genovese
Dec 21, 2020 · The "bcftools view" command provides conversion between the text VCF and the binary BCF format, where both formats can be either plain (uncompressed) or block-compressed with BGZF for random access and compact size. The plain text VCF output is useful for visual inspection, for processing with custom scripts, and as a data exchange format.
You can try something like this in bcftools, which is a bit quicker than VCFtools, as it uses block gzipping and indexing. # make sure both files are indexed and in bgzip format bcftools index vcfA.vcf.gz bcftools index vcfB.vcf.gz # find overlapping positions between the two files bcftools isec -n~11 -c all vcfA.vcf.gz vcfB.vcf.gz > sharedPositions.txt # filter vcf files for the overlapping ...
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