GWAS summary statistics imputation support data and integration with PrediXcan MASHR

<p># GWAS summary statistics imputation, integration with PrediXcan MASHR-M</p> <p>&nbsp;</p> <p>The file `sample_data.tar` contains all necessary files to perform imputation of GWAS summary statistics to the GTEx v8 QTL data set.</p> <p>It includes 1000 Genomes individuals&#39; genotypes as reference panel.</p> <p>The `.tar` archive, upon uncompression, contains the following folder structure:</p> <p>```</p> <p>data<br> |-- coordinate_map<br> |-- gwas<br> |-- liftover<br> |-- models<br> |&nbsp;&nbsp; |-- eqtl<br> |&nbsp;&nbsp; |&nbsp;&nbsp; `-- mashr<br> |&nbsp;&nbsp; `-- sqtl<br> |&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; `-- mashr<br> |-- reference_panel_1000G<br> `-- ucsc</p> <p>```</p> <p>&nbsp;</p> <p>`data/eur_ld.bed.gz` contains definitions of approximately independent LD-regions in hg38 (Berisa-Pickrell regions, lifted over)</p> <p>`data/gtex_v8_eur_filtered_maf0.01_monoallelic_variants.txt.gz` is a snp annotation file, listing all GTEx v8 variants with MAF&gt;0.01 in europeans.</p> <p>`data/coordinate_map` contains precomputed mapping tables that MetaXcan tools can use to convert GWAS&#39; genomic coordinates in GWAS between genome assemblies.</p> <p>`data/gwas` contains a sample GWAS file for the purposes of a tutorial (data obtained from Nikpay et al (Nat Gen 2016) https://www.ncbi.nlm.nih.gov/pubmed/26343387</p> <p>`data/liftover` contains Liftover chains to map coordinates between human genome assemblies (used by full harmonization tools)</p> <p>`data/models` contains PrediXcan MASHR-M models, and cross-tissue S-MultiXcan LD compilation, from eQTL and sQTL.</p> <p>`data/reference_panel_1000G` contains 1000G hg38 genotypes, in parquet format, to be used by imputation tools.</p> <p>`data/ucsc` contains genomic coordinates of rsids in hg17, hg18 and hg19. You can use these to add chromosome and start position information to a GWAS based on its rsids. (column `end` is not used)</p> <p>&nbsp;</p>