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dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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GLnexus.DB #236

Open xshah opened 3 years ago

xshah commented 3 years ago

Does glnexus only load variants contained in the bed file into the db? or all of the variants?

mlin commented 3 years ago

Everything in the input gvcf files is loaded into the database, the bed file controls what is processed thereafter. Therefore, if you want to split up jobs e.g. by chromosome then it can be advantageous to slice up the gvcf files with tabix before using with glnexus_cli.