Chunk #49 — Findings — Improvements in PLINK 1.9 — Convenience features — Unplaced contig and nonhuman species support

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Second-generation PLINK: rising to the challenge of larger and richer datasets.

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When the –allow-extra-chr or –aec flag is used, PLINK 1.9 allows datasets to contain unplaced contigs or other arbitrary chromosome names, and most commands will handle them in a reasonable manner. Also, arbitrary nonhuman species (with haploid or diploid genomes) can now be specified with –chr-set.