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As part of our [genotypes and variants super ticket](https://github.com/monarch-initiative/monarch-app/issues/715) we identified that we want to confirm that our pipeline that brings in genotypes from…
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Thank you so much for your fast response to the previous issue. I am currently applying the GIFT_summary function on a real data example. The true causal gene should be gene4. The input for GIFT_summa…
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### A clear description of your feature request
Calculation of linkage disequilibrium via phased data and comparing phased and unphased LD via a Sign test. Also for 2-locus haplotypes, calculation of…
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Dear developers:
I was wondering that how to prepare a VCF for vartrix if I want to get variation information for a specific region per base.
For example , I want to get all variation information f…
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From Adriana/MedGen (email: MedGen reports on CUI conflicts with Mondo data)
Medgen serves the clinical community by enabling discovery of phenotype information and it also serves as the phenotype …
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Currently, the [mutators](https://github.com/kipoi/kipoi/blob/master/kipoi/postprocessing/variant_effects/utils/mutators.py) accepts pandas arrays as arguments for the `__call__` method:
```python
…
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Dear Mike,
Thanks for your previous help! I successfully run the tool on a human sample and get the output `IGHV_functional_allele_calls.txt`, but I am curious what does the output mean. Specifical…
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How do isoforms relate to genotypes?
This genotype looks like it's isoform specific because the three isoforms of prp10 have different sequences:
https://www.pombase.org/genotype/prp10-1-A1089V,S1…
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Hi,
I have some questions about pruning step (how heterozygous alleles be partitioned...) and input/output files.
1. What is the difference between collapsed regions and chimeric contigs in prunin…
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Hi Brad,
I am assuming the recall jar uses optimized parameter settings for the variant caller based on bcbio settings. I've been looking at exploring incremental join calling on tumour only samples.…