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=== Genotype ===
=== Genotype ===
Genotypes variants for each sample.
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#merge duplicate variants and save output in mills.merged.vcf
#genotypes variants found in candidate.sites.vcf from sample.bam
vt mergedups mills.vcf -o mills.merged.vcf
vt genotype -r seq.fa -b sample.bam -i candidates.sites.vcf -o sample.sites.vcf
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usage : vt genotype [options]
options : -r reference sequence fasta file []
-s sample ID []
-o output VCF file [-]
-b input BAM file []
-i input candidate VCF file []
-- ignores the rest of the labeled arguments following this flag
-h displays help
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