polyfun

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Alternative to HESS estimate

1

Hi Omer, I have a recommendation to substitute for HESS generated priors in the SuSie workflow. We discussed on other different threads as to how this causes issue with small...

jerome-f

Compute LD-scores for each SNP bin using .bcor files

16

Hi, I am interested in creating priors with PolyFun using approach 3. I would like to pass estimates of LD from the data I have, stored in .bcor files. Is...

JoniColeman

Assertion Error when using functional susie fine mappping

7

Hi Omer, Can I know if we have some advice on how to fix this AssertionError ? : ------------------------------------------------------------------------------------------------------------------------------ Traceback (most recent call last): File "/filepath/finemapper.py", line 1262, in residual_var=args.susie_resvar,...

dietina

## Overview We have processed the GWAS summary statistics for many dozens of traits using a pipeline that performs functionally-informed fine-mapping with PolyFun. Overall this has been very successful (thanks...

jdblischak

Can PolyFun be applied to eQTL summary statistics from multiple genes

1

I understand that PolyFun (Nat Genet, 2020) was developed to estimate prior causal probability based on functional annotation by using summary statistics for a single trait. Now we have cis-eQTL...

gmgaous

MAF munging

5

# munge_polyfun_sumstats.py In line 62 I noticed that when the columns are renamed, freq and MAF seem to be treated the same. But couldn't these two things be different in...

bschilder

MAF for cases and controls

1

Hello! First off thank you for this amazing package/pipeline! I had a question regarding my summary statistics. I have a column for MAF for cases and MAF for controls, but...

RaviBot

about missing annotations for rare variants

3

Dear Omer, I am planning to apply PolyFun + SuSiE by including our own functional annotation data (~10 different types) predicted by deep learning model. However, we only have predictions...

szhan1000

HI, I noticed that in the WIKI about PolyPred, the result generated by the parameter --predBetasFile in bolt-lmm was used as an estimate of the effect size of the tag...

Y-Isaac

Issues on the number of chromosomes in different species

2

Hello, thank you very much for the development and maintenances of the PolyFUN program. I have engaged in conducting finemapping on the pig genome using the PolyFun because the functional...

heebokp