Generally VCF files are accompanied by an index file, and from this file the number of variants can be obtained. For example with bcftools: bcftools index --nrecords <in.vcf.gz>
This could be used to speed up the seqVCF2GDS function by avoiding the variant counting step. As this step is currently single threaded, it contributes significantly to the run-time when converting large VCF files.
Generally VCF files are accompanied by an index file, and from this file the number of variants can be obtained. For example with bcftools:
bcftools index --nrecords <in.vcf.gz>This could be used to speed up the seqVCF2GDS function by avoiding the variant counting step. As this step is currently single threaded, it contributes significantly to the run-time when converting large VCF files.