.loom file generation algorithm

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The post-processing steps after variant calling include variant decomposition, filtering, and output file generation.

Multiallelic variants are decomposed into biallelic variants and then normalized to ensure that each VCF entry is left-aligned and parsimonious (Tan, Abecasis, et al. 2015). Blacklisted loci (suspected false variants) are filtered out, and all loci that are more than the 1000 QUAL threshold are tagged for downstream processing. The positions that pass our filtering criteria are called variants. The genotypes and the cell matrix are converted into an open-source .loom format (Zeisel, Hochgerner, et al. 2018), which allows efficient storage, data retrieval, and sharing of large omics datasets.

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