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@Cristianetaniguti Cristianetaniguti released this 29 Nov 19:52
· 210 commits to main since this release
SimulatedReads2Map_v1.0.0
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Learn about vigilant mode.

1.0.0

Initial release

This workflow perform simulations of one or more (defined by number_of_families) bi-parental outcrossing population haplotypes using PedigreeSim software based on a provided linkage map and SNP markers. It uses RADinitio software, the simulated haplotypes and a reference genome to also simulate genotyping-by-sequencing read sequences. After, it performs the SNP and genotype calling and builds 68 linkage maps from the combinations:

  • SNP calling: GATK and Freebayes
  • Dosage/genotype calling: updog, polyRAD and SuperMASSA
  • Linkage map build software: OneMap 3.0 and GUSMap
  • Using genotype probabilities from GATK, Freebayes, updog, polyRAD and SuperMASSA, and a global error rate of 5% and 0.001% in the OneMap HMM.

It also has the options to:

  • Include or not multiallelic (MNP) markers
  • Apply filters using VCFtools

This workflow uses:

  • A reference linkage map
  • A reference VCF file
  • A single chromosome from a reference genome
  • Diploid bi-parental F1 population
  • Genomic positions for markers order
Assets 5
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