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gwasvcf

ANALYTICS
Velocity0.0

Tools for Dealing with GWAS Summary Data in VCF Format

github.com/MRCIEU/gwasvcf ↗

gwasvcf has stopped adding features and now just keeps proxy matching from failing.

rgenomicsgwasbioinformaticsmaintenance
◆Current state
gwasvcf reads and queries GWAS summary statistics stored as VCF, with LD proxy lookup as its most-used entry point. Every release in the visible window is a fix, and all but one land in or around proxy_match(). The last functional addition was gwasvcf_to_summaryset() in 0.1.2, which hands data to gwasglue2 rather than doing new work here.
◆Where it's heading
The package is in custodial maintenance inside the MRC IEU OpenGWAS stack, and its releases are reactive: each one answers a specific user-reported failure, credited to the reporter. The 0.1.6 pattern is telling — rather than replace the proxy VCF construction, it keeps the original path and adds a fallback only for inputs that fail, so existing results are left bit-for-bit unchanged.
◆Prediction
Expect further narrow robustness fixes to proxy_match() driven by user-reported VCF shapes; nothing in the entries suggests new analysis capability is being built here rather than in gwasglue2.

◆Recent moves

  1. 5mo ago

    proxy_match() gains a fallback VCF construction path

    proxy_match() now catches failures in its VCF construction and retries through a compatibility path that extracts genotypes as matrices, flips effect signs and inserts the PR matrix before building the VCF once. Successful cases keep the original code path untouched, which is a deliberate choice to avoid perturbing existing results.

    View source ↗
  2. 8mo ago

    proxy_match() handles multi-sample VCFs

    Makes proxy_match() robust to VCFs carrying multiple samples. Another user-reported input shape the function did not handle, in the same function 0.1.6 would revisit months later.

    View source ↗
  3. 1y ago

    sqlite3 declared in SystemRequirements

    Declares sqlite3 in SystemRequirements for the p-value index builder and refreshes documentation URLs. Packaging metadata only.

    View source ↗
  4. 1y ago

    Message fix in get_ld_proxies()

    A message fix in get_ld_proxies(), published the same day as 0.1.4. No behavioral change.

    View source ↗
  5. 2y ago

    gwasvcf_to_summaryset() bridges to gwasglue2

    Adds gwasvcf_to_summaryset() to hand VCF contents to gwasglue2 as a SummarySet, plus a tibble deprecation fix. This is the last feature addition in the record, and it points analysis work out of this package rather than into it.

    View source ↗