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jeromekelleher merged 2 commits into from
Aug 13, 2019
Merged

Alpha4 changes #300

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820dc80
Documented allele values in VCF.
jeromekelleher Aug 13, 2019
6215743
Bumped version to alpha 4.
jeromekelleher Aug 13, 2019
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2 changes: 1 addition & 1 deletion python/tskit/_version.py
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@@ -1,3 +1,3 @@
# Definitive location for the version number.
# During development, should be x.y.z.devN
tskit_version = "0.2.0a3"
tskit_version = "0.2.0a4"
11 changes: 10 additions & 1 deletion python/tskit/trees.py
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Expand Up @@ -3048,7 +3048,16 @@ def write_vcf(
Each individual in the output is identified by a string; these are the
VCF "sample" names. By default, these are of the form ``tsk_0``,
``tsk_1`` etc, up to the number of individuals, but can be manually
specified using the ``individual_names`` argument.
specified using the ``individual_names`` argument. We do not check
for duplicates in this array, or perform any checks to ensure that
the output VCF is well-formed.

The REF value in the output VCF is the ancestral allele for a site
and ALT values are the remaining alleles. It is important to note,
therefore, that for real data this means that the REF value for a given
site **may not** be equal to the reference allele. We also do not
check that the alleles result in a valid VCF---for example, it is possible
to use the tab character as an allele, leading to a broken VCF.

The ``position_transform`` argument provides a way to flexibly translate
the genomic location of sites in tskit to the appropriate value in VCF.
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