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Is there any parameter to determine sex when calling cnv in human? I noticed the parameter "--haploid-chr arg haploid chromosomes, e.g. chrX,chrY". Could this be helpful?
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In comparing output from the API and the CLI during the probgen workshop I noticed a discrepancy in the ploidy output through a conversion to vcf. I think the issue is on the CLI side.
Here's an e…
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Hi all,
we are assembling some haploid fungal genomes (using PacBio HiFi data). Would purge_dups be appropriate for removing contig overlaps in such an assembly?
Best,
Ricardo Ramiro
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I assume that if this is haploid data, we don't need a call_genotype_phased array to show that the data is phased? Unless the suggestion is that haploid data without a call_genotype_phased array could…
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Hello,
I am interested in using the locator algorithm for haploid organisms. The help text says to file an issue.
Thank you,
Mike
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Hello, I want to use haploid data (Y microsatellites) for EBSP analysis.
however I cannot find how to set the ploidy.
Also, I tried to use the template provided by the vntr package but Beauti only…
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### Description of feature
It is unclear if this pipeline will work on any organism assembly?
Is it haploid genomes only?
Is it especially for bacteria?
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Hello,
I was trying to use gtcheck for haploid data. I skimmed through the code of the function and saw various mentions about diploidy. Can you confirm that gtcheck does not work for anything ot…
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Can haploid data be used with OutFLANK? I'm assuming no, as I don't see a MakeHpploidFSTMat function, but I thought I'd double-check.
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### Description of feature
**Description**:
I am writing to request the addition of parameters for specifying haploid contigs and regions when detecting SNPs and Indels using DeepVariant in the nf…