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VCFArrow 0.9.0

• Initial CRAN submission.

Reading and storage

• read_vcf() reads plain or gzip-compressed VCF files (including large DiscoSnp-RAD output) into a VCFArrow S4 object. Variant information is kept in memory; genotypes are written to disk as an ‘Apache Arrow’ dataset in chunks and read lazily, so datasets larger than memory can be processed.
• set_vcf_groups() assigns samples to groups (populations); vcf_copy() makes an independent copy; vcf_gc() deletes the on-disk data of objects that are no longer referenced.
• vcf_memory_estimate() estimates the memory an export needs, and vcf_suggest_chunk_size() suggests a chunk size for read_vcf() for the available memory.

Filtering, subsetting and merging

• Variant filters: vcf_filter_quality(), vcf_filter_pass(), vcf_filter_biallelic(), vcf_filter_indels(), vcf_filter_coverage(), vcf_filter_maf(), vcf_filter_hets(), vcf_filter_missingness(), vcf_filter_invariant(), vcf_filter_oneSNV() and vcf_filter_multiSNV() (SNV blocks), and, for DiscoSnp-RAD data, vcf_filter_rank(), vcf_filter_rpt() and vcf_filter_paralogs().
• Sample filters and subsets: vcf_filter_missing(), vcf_extract_samples(), vcf_extract_groups(), vcf_sub_SNVs() and vcf_sub_SNVs_stratified().
• vcf_filter_adr() corrects or removes genotypes with an extreme allele depth ratio (ALT / (REF + ALT)): they are changed to homozygous or set to missing.
• vcf_bind() merges objects with the same or different samples, matching variants by CHROM, POS, REF and ALT, in "intersect" or "union" mode, with an ingroup/outgroup mode (outgroup = TRUE) and optional recovery of previously filtered loci (recover_loci = TRUE). vcf_bind_sparse() is a deprecated alias of vcf_bind(..., recover_loci = TRUE).

Statistics and plots

• vcf_stats() computes per-sample statistics (heterozygosity, missing data, depth) and, optionally, Watterson’s theta and nucleotide diversity per group (vcf_theta()), accumulated chunk by chunk with little memory.
• assess_vcf_missing_data() writes a table and plots of missing data per sample, and assess_vcf_coverage() plots of read depth per sample (PDF, PNG and SVG).

Writing and conversion

• write_vcf() writes plain or gzip-compressed VCF files.
• Converters to the input formats of population-genetic and phylogenetic software: vcf2admixture(), vcf2apparent(), vcf2arlequin(), vcf2bayesass(), vcf2bayescan(), vcf2eigenstrat(), vcf2fasta(), vcf2fineradstructure(), vcf2genepop(), vcf2migrate(), vcf2nexus(), vcf2plink_bed(), vcf2plink_ped(), vcf2related(), vcf2smartsnp(), vcf2snapp(), vcf2snmf(), vcf2structure() and vcf2treemix(); vcf2gt_long() writes a long genotype table (CSV, feather or Parquet) and vcf2genlight() returns an ‘adegenet’ genlight object.

Performance

• vcf_set_workers() runs the per-chunk work of reading, filtering, statistics, merging and exporting on background R processes. Results do not depend on the number of workers.
• Performance-critical steps (VCF parsing, per-sample counts, theta and pi, writers of the exported formats) are implemented in C++.

Dependencies

• ‘adegenet’ (for vcf2genlight()) and ‘svglite’ (for SVG plots) are suggested rather than imported; without ‘svglite’, SVG plots are written with R’s Cairo device.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.