Splice altering variant predictions in four archaic hominin genomes

This file contains high-quality autosomal SNVs that occur among four high-coverage archaic genomes aligned to the hg19/GRCh37 reference genome. Each entry corresponds to a single variant with a distinct GENCODE, Human Release 24, annotation per genomic position. Data per variant includes the genomic position, reference/alternate alleles, archaic genotypes, gene annotation, and additional data relevant to the analysis of splicing variants:

SpliceAI annotations
gene constraint measured using data from gnomAD
variant conservation measured using phyloP
allele origin
allele frequencies in modern humans from the Thousand Genomes Project and gnomAD
introgression metadata
sQTL data from GTEx

Methods
All data in this file are publicly available (see below). Archaic variants were filtered using bcftools to retain high-quality sites and high-quality genotypes. Missing data and irrelevant fields per variant are marked as "n/a". Only variants matching a filtered archaic variant were included from the other datasets (see below). The dataframe was created using Pandas in a Python Jupyter notebook.

Data used in this notebook:

Altai Neanderthal SNVs (http://ftp.eva.mpg.de/neandertal/Vindija/VCF/Altai/)
Browning et al. 2018 Introgressed Variants (https://data.mendeley.com/datasets/y7hyt83vxr/1)
Chagyrskaya Neanderthal SNVs (http://ftp.eva.mpg.de/neandertal/Chagyrskaya/VCF/)
Denisovan SNVs (http://ftp.eva.mpg.de/neandertal/Vindija/VCF/Denisova/)
gnomAD allele frequencies (https://gnomad.broadinstitute.org/downloads#v3-variants)
gnomAD constraint (https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz)
phyloP (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/primates.phyloP46way.bw)
sQTLs (https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_sQTL.tar)
Thousand Genomes Project (http://hgdownload.soe.ucsc.edu/gbdb/hg38/1000Genomes/)
Vernot et al. 2016 Introgressed Tag SNPs (https://drive.google.com/drive/folders/0B9Pc7_zItMCVM05rUmhDc0hkWmc?resourcekey=0-zwKyJGRuooD9bWPRZ0vBzQ)
Vindija Neanderthal SNVs (http://ftp.eva.mpg.de/neandertal/Vindija/VCF/Vindija33.19/)