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Convert the workflow [allele-specific-expression](https://github.com/icgc-argo-workflows/allele-specific-expression) to follow `nf-core` structure and guideline.
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I noticed that the py-ard implementation for converting v2 to v3 typings is not yet complete:
https://github.com/nmdp-bioinformatics/py-ard/blob/d43a035361cc90cef9bf0c98475ec90396b06a4f/pyard/db.py…
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There is a point where GenotypeGVCFs corrects PGTs of 0|1 or 1|0 for homozygous variant events, but they do contain different haplotypes in some cases. Revert this "correction" so we don't lose/falsi…
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Hey, I am trying to do allele-specific expression analysis (ASE) for a few RNA seq samples ( 32 disease and 5 normal samples, unpaired unrelated). Could you suggest a pipeline/method to convert the ma…
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So we can change allele freq in the founders (not setting to 0.5 and not estimating from the data)
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Hi,
I am intersected in a region in chr6 and I only have the SNP information in this region. Can I used the allele-specific mode to study the differences of contacts between two alleles in this regi…
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Hi,
I have a few questions related to the phasing options.
1. Why is the default SNP panel limited to these variants: "7.4M SNPs with minor allele frequency (MAF) > 0.05:"? If I have tumor data …
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Hi, I have a question about how reads are assigned as conflicting, unassignable etc.
I've been trying to use SNPsplit on noisy PacBio long reads to help with haplotype-resolved assembly (which I kn…
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Hello,
In large cohorts (~100K) multi-allelic sites are very common. Furthermore, good rare alleles can share the locus of bad, "common" variants (they are common since they seem to appear in many in…
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The field should contain the following information
embryo production (mating, superovulation & mating, IVF)
Email from LN: March 3, 2021 at 2:05 PM
Hi All,
I thought we had agreed to capture the v…