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Fig. 3 | BMC Bioinformatics

Fig. 3

From: GenESysV: a fast, intuitive and scalable genome exploration open source tool for variants generated from high-throughput sequencing projects

Fig. 3

Benchmarking of VCF data import. Comparison of VCF importation between GenESysV and GEMINI. For comparison purposes, data importation performance for Annovar annotated VCF files is also shown in this figure. The phase3 VCF file from the 1000 Genomes Project is downloaded and annotated with VEP or Annovar. A series of VCF files containing the full or subsets of variants is generated by including variants from the first 100, 250, 500, 750, 1000, 1250, 1500, 1750, 2000 samples. These VCF files are used as inputs for importation using the data loading script (load_vcf.py) in our GenESysV package. These tests were performed using a server computer with 24 CPU cores (Intel(R) Xeon(R) CPU E5–2620 v3 @ 2.40GHz) and 128 GB memory (max heap size for Java virtual machine was set to 31 GB using the –Xmx flag, as recommended by the Elasticsearch documentation)

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BMC Bioinformatics

ISSN: 1471-2105

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