Skip to content

EmpiricalMaps_v1.0.0
Compare
Choose a tag to compare
@Cristianetaniguti Cristianetaniguti released this 25 Nov 19:10
· 215 commits to main since this release
EmpiricalMaps_v1.0.0
f05da13
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

1.0.0

Initial release

This workflow receives as input VCF files from EmpiricalSNPCalling workflow and result in 34 linkage maps for a single chromosome running 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:

  • Diploid bi-parental F1 population
  • Genomic positions for markers order
Assets 5
Loading