File: cells.loom

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This file is an input file for Tapestri Insights. LOOM is an efficient file format for very large omics datasets, consisting of a main matrix, optional layers, and a variable number of row and column annotations. We added multiple layers to accommodate single-cell genotype data.

The LOOM file generated by the DNA Pipeline has 5 layers. 

NGT (numerical genotype) is the default layer that is stored as the main matrix.

The other 4 layers are AD (number of reads with evidence for mutation), DP (read depth), GQ (genotype quality), and RO (number of reads with no evidence for mutation). It also has the barcodes as the column attributes of the .loom file, and the variant information is present in the row attributes.

For all barcodes called as cells, it contains metadata for all the variants, including their position, type, and annotations.

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