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notebook-simulation.trees | ||
notebook-simulation.samples | ||
notebook-simulation-source.trees | ||
notebook-simulation.vc* | ||
notebook-simulation-AA.npy | ||
P_dom_chr24_phased.samples | ||
sparrows.vcz |
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{ | ||
"contigs": [ | ||
"0" | ||
], | ||
"source": "sgkit-0.9.0" | ||
} |
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{ | ||
"zarr_format": 2 | ||
} |
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{ | ||
"metadata": { | ||
".zattrs": { | ||
"contigs": [ | ||
"0" | ||
], | ||
"source": "sgkit-0.9.0" | ||
}, | ||
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"_ARRAY_DIMENSIONS": [ | ||
"variants", | ||
"samples", | ||
"ploidy" | ||
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"comment": "A flag for each call indicating which values are missing.", | ||
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"comment": "A flag for each call indicating if it is phased or not. If omitted\nall calls are unphased.", | ||
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], | ||
"comment": "The possible alleles for the variant." | ||
}, | ||
"variant_contig/.zarray": { | ||
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"comment": "Index corresponding to contig name for each variant. In some less common\nscenarios, this may also be equivalent to the contig names if the data\ngenerating process used contig names that were also integers." | ||
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"_ARRAY_DIMENSIONS": [ | ||
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], | ||
"comment": "The reference position of the variant." | ||
} | ||
}, | ||
"zarr_consolidated_format": 1 | ||
} |
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---|---|---|
@@ -0,0 +1,9 @@ | ||
{ | ||
"_ARRAY_DIMENSIONS": [ | ||
"variants", | ||
"samples", | ||
"ploidy" | ||
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"comment": "Call genotype. Encoded as allele values (0 for the reference, 1 for\nthe first allele, 2 for the second allele), -1 to indicate a\nmissing value, or -2 to indicate a non allele in mixed ploidy datasets.", | ||
"mixed_ploidy": false | ||
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---|---|---|
@@ -0,0 +1,24 @@ | ||
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,9 @@ | ||
{ | ||
"_ARRAY_DIMENSIONS": [ | ||
"variants", | ||
"samples", | ||
"ploidy" | ||
], | ||
"comment": "A flag for each call indicating which values are missing.", | ||
"dtype": "bool" | ||
} |
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docs/_static/example_data.vcz/call_genotype_phased/.zarray
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---|---|---|
@@ -0,0 +1,8 @@ | ||
{ | ||
"_ARRAY_DIMENSIONS": [ | ||
"variants", | ||
"samples" | ||
], | ||
"comment": "A flag for each call indicating if it is phased or not. If omitted\nall calls are unphased.", | ||
"dtype": "bool" | ||
} |
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