Entering edit mode
2.9 years ago
lz1903
▴
10
Hi,
I have tried to split vcf into multiple file with following codes:
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
But it gives me error: Could not parse argument: --compression-level $file
What does it mean, how can I get rid of it. Thanks in advance!
what is your shell ? what is the output of ${SHELL} ? are you using bash ? replace "bcftools view" with "echo" , what is the output ?