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Thank you for developing and maintaining nf-gwas.
I was wondering about support for chromosome X analysis. When providing input as vcf.gz, with male coding 0 2, nf-gwas worked in my hands. However, annotation did not work. I specified the encoding of the sex chromosome as X, default in plink2, but nf-gwas seems to use 23 in the output result (previous default in plink1.9), which supposedly did not match the X-encoded snp reference table of the file provided to nf-gwas rsids_filename, probably resulting in the non-annotation of the chromosome X results in the interactive output.
So I was wondering if chr X analysis is currently supported or documented anywhere, as also the example result on github only show results from autosomes.
Thanks very much,
Holger
The text was updated successfully, but these errors were encountered:
Thank you for developing and maintaining nf-gwas.
I was wondering about support for chromosome X analysis. When providing input as vcf.gz, with male coding 0 2, nf-gwas worked in my hands. However, annotation did not work. I specified the encoding of the sex chromosome as X, default in plink2, but nf-gwas seems to use 23 in the output result (previous default in plink1.9), which supposedly did not match the X-encoded snp reference table of the file provided to nf-gwas rsids_filename, probably resulting in the non-annotation of the chromosome X results in the interactive output.
So I was wondering if chr X analysis is currently supported or documented anywhere, as also the example result on github only show results from autosomes.
Thanks very much,
Holger
The text was updated successfully, but these errors were encountered: