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Suggestion: seqVCF2GDS could use index file to get total number of variants

Open jemunro opened this issue 5 years ago • 0 comments

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.

jemunro avatar Jul 01 '19 01:07 jemunro