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posted on 2023-11-30, 08:23 authored by Paul M. VanRaden

The findmap.f90 program aligns sequence reads to reference map, calls previous variants, and identifies new variants. Program and download information can be found at the Animal Improvement Program (AIP) web site:

Sequencing research requires efficient computation. Few programs use already known information about DNA variants when aligning sequence data to the reference map. New program findmap.f90 reads the previous variant list before aligning sequence, calling variant alleles, and summing the allele counts for each DNA source in a single pass. Advantages are faster processing, more precise alignment, more useful data summaries, more compact output, and fewer steps. Programs findmap and BWA were compared using simulated paired end reads of length 150 from fragments of length 1,000 at random locations within the UMD3.1 bovine reference assembly. Each base had 1% probability of error and 1% probability of missing. The 39 million variants from run 5 of the 1,000 bull genomes project were included, with every other variant set to reference or alternate. With 1 processor, BWA required 629 minutes per 1X for alignment, whereas findmap required 12 minutes per 1X for alignment and variant calling. Percentage of correctly mapped reads was 90.5% from BWA and 92.9% from findmap. Variant calls were output by findmap only for the 88.2% of pairs where both ends were located within the fragment length and of opposite orientation. Percentages of variants called correctly were 99.8% for SNPs and 99.9% for deletions, while insertions had 99.9% of alternate calls correct but only 98.6% of reference calls. Memory required by BWA was 4.6 Gbytes / processor, whereas findmap required 46 Gbytes that could be shared by multiple processors. Simultaneous alignment and variant calling is an efficient and accurate strategy.

Resources in this dataset:


Agricultural Research Service


Data contact name

Hubbard, Suzanne

Data contact email


United States Department of Agriculture


  • Not specified

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

computer software; models; animals; genome; computers; memory; humans; autosomes; mitochondrial DNA; homozygosity; alleles; heterozygosity; single nucleotide polymorphism; reading; bulls; DNA; probability

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

VanRaden, Paul M. (2019). FINDMAP. United States Department of Agriculture.