I have to split a multisample VCF (the output of GATK4) into single vcfs (per sample). What is the best code? Then I have to annotate them with AnnovaR.
vcf-subset -c samplename -e inputvcf > sample.vcf bcftools view -Oz -s samplename inputvcf > sample.vcf.gz
Is it correct to add the -e option in the vcf-subset code? or I'm going to lose data?