Updates on Benchmark

[LiangdeLI]

This is for the updates of the benchmark work, will keep updating by 'timestamps:

Summary of done:

20210527: Catching up on what Shaoqing left.

20210610: Missed the meeting, clashed with a final exam.

20210624: Learning and trying out of sgkit and Hail code.

20210708: Learning and trying PLINK, checkout SLAB source code. Met with Arun, discussed the plan.

20210722: Done single node benchmark of allele frequency/variant stat on 1000 Genomes chr21 data.

20210819: Could not attend as clashed with VLDB conference ongoing.

20210902: Can not attend as flying to CA.

Done since last meeting:
Figured out the way to have all tools reading in their default data format. Used bcftools to concat 1000genomes into 1 .vcf and convert to .bed, .mt, .zarr. Solved some runtime issues because the large volume of data on the cluster. Implementing more genome algorithms in the benchmark pipeline.

Goal:
Try to have experiments done in September.