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How To Split Vcf Files

I have a vcf file with 60 animals (columns) and I would like to split these animals in 10 subset with 6 animals chosen randomly per group. I'm using the following script, but it's not working:

head -n 60 my.vcf | grep "^#" > header

grep -v "^#" out.subgrupos.vcf > animals

split -l 6 animals

for i in x*;do cat header $i >$i.vcf && rm -f $i;done

rm -f header animals

I need to keep the header in each file. Is there another way to do that?

vcf vcftools
• 2,146 views • link
updated by likame8586 • likame8586 • written by mayara_salvian • mayara_salvian

1 answer 

grep '#CHROM' -m1 my.vcf | cut -f 10- | tr "\t" "\n" | shuf | split -l 6 - animal
for F in animal*
do
     bcftools view --samples-file $F my.vcf > "split.${F}.vcf"  && rm "${F}"
done
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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