Coloc/Enloc of GTEx v8

[Robert Butler]

Hello,

I am following along with the MetaXcan workflow, and want to run Coloc for a list of traits (Harmonized via the tutorial), on the GTEx v8 tissues (specifically the brain phenoytpes).

1. Is there an easy source for the GTEx v8 tissues that are already in the necessary format for the run_Coloc script? or is it starting from the allpairs file?

2. I couldn't find the script to generate the Enloc priors in the summary-gwas-imputation or the gtex-gwas-analysis githubs. I noticed coloc now uses susie for multiple causal variants, with LD information provided? Is that now implemented instead?

Thanks,

Robert Butler 

[Hae Kyung Im]

cc'ing the mailing list (I forgot to do that in my previous reply). Alvaro may be able to respond to your question.

Haky

On Wed, Oct 13, 2021 at 12:46 PM Robert Butler <rrbut...@gmail.com> wrote:

Thanks Haky!

I was trying to generate the input gwas pip files for enloc using my harmonized & imputed GWAS sets, and i was wondering if the script dap_on_summary_stats.py can do this? It looks like I can use that with the reference_panel_1000G parquet files to get the LD information?

Looking like this:

```

python $REF/summary-gwas-imputation/src/dap_on_summary_stats.py \
  -parquet_genotype $REF/reference_panel_1000G/variants.parquet \
  -parquet_genotype_metadata $REF/reference_panel_1000G/variant_metadata.parquet \
  -summary_stats $GWAS/$TYPE/${PHENO}_harmonized.txt.gz \
  -output_folder DAP-g

```

As a side question, is there an easy way to combine/split the chromosomal parquet files into one file?

Thanks,

Robert Butler

On Tue, Oct 12, 2021 at 6:42 AM Hae Kyung Im <ha...@uchicago.edu> wrote:

Hi Robert,

You may try using fastENLOC which provides all the eQTL input files. https://github.com/xqwen/fastenloc

Haky

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Hae Kyung Im, PhD - 任慧耕 - 임혜경 - She/her
Assistant Professor, Section of Genetic Medicine
The University of Chicago Medicine & Biological Sciences
Member of Committee on Genetics, Genomics & Systems Biology
Center for Translational Data Science

Computing Environment and Life Sciences Directorate, Argonne National Laboratory
5841 S. Maryland Ave. Chicago, IL 60637, USA| N412
Phone:  773.702.3898 | FAX: 773.702.2567
Email: ha...@uchicago.edu | Twitter: @hakyim
http://hakyimlab.org | https://github.com/hakyimlab | https://orcid.org/0000-0003-0333-5685
http://scholar.google.com/citations?user=1QD4sIcAAAAJ
Directions to my office https://tinyurl.com/hki-office

--

Robert R Butler III, PhD

Senior Research Scientist

Stanford University School of Medicine

p: (612) 669-4586 | LinkedIn | ORCiD | @rrbiiiphd

--

Hae Kyung Im, PhD - 任慧耕 - 임혜경 - She/her
Assistant Professor, Section of Genetic Medicine
The University of Chicago Medicine & Biological Sciences
Member of Committee on Genetics, Genomics & Systems Biology
Center for Translational Data Science

Computing Environment and Life Sciences Directorate, Argonne National Laboratory
5841 S. Maryland Ave. Chicago, IL 60637, USA| N412
Phone:  773.702.3898 | FAX: 773.702.2567
Email: ha...@uchicago.edu | Twitter: @hakyim
http://hakyimlab.org | https://github.com/hakyimlab | https://orcid.org/0000-0003-0333-5685
http://scholar.google.com/citations?user=1QD4sIcAAAAJ
Directions to my office https://tinyurl.com/hki-office