Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

seqGDS2SNP() altering genotype values for haploid data #42

Open
AAvalos82 opened this issue Jan 30, 2019 · 1 comment
Open

seqGDS2SNP() altering genotype values for haploid data #42

AAvalos82 opened this issue Jan 30, 2019 · 1 comment

Comments

@AAvalos82
Copy link

Came across an issue where using seqGDS2SNP() on a "SeqVarGDSClass" object housing haploid variant calls that had been filtered. Effectively the process alters the genotypes, with the resulting "SNPGDSFileClass" object's genotype matrix not matching at all to the source data (even missing values are replaced). Extracting the genotype array from the source "SeqVarGDSClass" object works fine, and so does extraction of the dosage matrix, both of these match each other (with the dosage value accounting for REF allele count as it should). However it seems that when seqGDS2SNP() parses through the "SeqVarGDSClass" genotype array it produces something else altogether.

I also tried to produce the "SNPGDSFileClass" object with the dosage = T option, and this resulted in:

Error in seqApply(gdsfile, dosage, as.is = gGeno, .progress = verbose, : The GDS node "annotation/format/DS/data" does not exist.

This may be an unrelated issue, but I thought it would be worth noting.

@complexgenome
Copy link

Were you able to resolve this?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants