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Chromosome X support in nf-gwas #110

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holgerman opened this issue Jan 25, 2025 · 0 comments
Open

Chromosome X support in nf-gwas #110

holgerman opened this issue Jan 25, 2025 · 0 comments

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@holgerman
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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

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