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[write_vcf] CHROM is "MTB_anc" #262

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jameshadfield opened this issue Nov 29, 2023 · 0 comments
Closed

[write_vcf] CHROM is "MTB_anc" #262

jameshadfield opened this issue Nov 29, 2023 · 0 comments

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@jameshadfield
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jameshadfield commented Nov 29, 2023 •
edited

The VCF chromosome is hardcoded as "MTB_anc":

treetime/treetime/vcf_utils.py

Line 497 in 9fdceaa

output = ["MTB_anc", str(pos), ".", refb, ",".join(uniques), ".", "PASS", ".", "GT"] + calls

In lieu of knowing the actual chromosome name, I think using '1' seems to be convention.

In augur's case, a VCF is read upstream of this so we should be able to use the chromsome name provided there, either by making TreeTime aware of it and exposing it within get_tree_dict, or as another argument to write_vcf.

I'm happy to implement this, but any suggestions on the best solution are welcome!
jameshadfield added a commit that referenced this issue Dec 12, 2023
@jameshadfield
[vcf] use metadata to influence write format
99a56a1 
This is only used if provided, otherwise we fall back to the default
ploidy of haploid (unchanged) and chromosome name of "1" (changed from
the previously hardcoded "MTB_anc"). Note that the spec states that
no-call genotypes should be encoded to reflect the ploidy (e.g. "./."
for diploid and "." only for haploid) which is a change from previous
behaviour.

Closes #262
@rneher rneher closed this as completed in 0a835e7 Jan 22, 2024
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