already stated here and here:

for file in *.vcf*; do
  for sample in `bcftools query -l $file`; do
    bcftools view -c1 -Oz -s $sample -o ${file/.vcf*/.$sample.vcf.gz} $file
  done
done

I wrote Biostar130456 https://github.com/lindenb/jvarkit/wiki/Biostar130456

$   curl -sL "https://raw.githubusercontent.com/arq5x/bedtools2/bc2f97d565c36a82c1a0b12f570fed4398001e5f/test/map/test.vcf" |\
    java -jar dist/biostar130456.jar -x -z -p "sample.__SAMPLE__.vcf.gz" 
sample.NA00003.vcf.gz
sample.NA00001.vcf.gz
sample.NA00002.vcf.gz

$ gunzip -c sample.NA00003.vcf.gz
(...)
##source=myImputationProgramV3.1
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA00003
chr1    10  rs6054257   G   A   29  PASS    AF=0.5;DB;DP=14;H2;NS=3 GT:DP:GQ:HQ 1/1:5:43
chr1    20  rs6040355   A   G,T 67  PASS    AA=T;AF=0.333,0.667;DB;DP=10;NS=2   GT:DP:GQ 2/2:4:35
chr1    130 microsat1   GTC G,GTCT  50  PASS    AA=G;DP=9;NS=3  GT:DP:GQ    1/1:3:40
chr2    130 microsat1   GTC G,GTCT  50  PASS    AA=G;DP=9;NS=3  GT:DP:GQ    1/1:3:40

You could do something with the new bcftools v1.1 like this:

bcftools query -H pooled.vcf.gz -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' --samples 'favoriteSample'

I don't think it keeps all the headers but it will give you the information you might want. If you don't want any headers at all, you can remove the -H.

Post not found