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6.0 years ago
emmanouil.a
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120
Hi,
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?
Best
If that particular sample doesn't contain a variant i.e either not called or "reference homozygous", it will not be printed, which makes sense.