A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi! Quick WisecondorX question :blush:
I built a reference with `--nipt` and included female and *male fetus NIPT samples* in the cohort. However, in the resulting `.npz`:
```
norm["has_male"]```
returns `False`.
I’m also trying to identify the *blacklist (masked bins) genomic coordinates* — i.e. the regions excluded across all samples in the reference. Does anyone know where these are stored in the `.npz` or how to extract them?
Has anyone seen `has_male=False` despite male fetus samples in the cohort? Any hints appreciated :pray:

I found a way with a script to extract a bed file but I do not understand why `has_male` returns `False`

I checked the code and indeed, if I use `--nipt`  then :
```if not args.nipt:
    if genders.count("M") &gt; 4:
        <http://logging.info|logging.info>("Starting male gonosomal reference creation ...")
        ...
    else:
        logging.warning(
            "Provide at least 5 male samples to enable normalization of male gonosomes."
        )```
`args.nipt = True`
It is why!