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@Cristianetaniguti Cristianetaniguti released this 29 Nov 19:52
· 210 commits to main since this release
EmpiricalReads2Map_v1.0.0
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Learn about vigilant mode.

1.0.0

Initial release

This workflow build linkage maps from genotyping-by-sequencing (GBS) data. The GBS samples are splitted into chunks to be run in different nodes and optimize the analyses. Set the number of samples by chunk in the 'chunk_size' input. Use 'max_cores' to define number of cores to be used in each node. The workflow runs 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.

Resulting in 34 linkage maps.

The workflow include de options to:

  • Remove or not the read duplicates
  • Perform the Hard Filtering in GATK results
  • Replace the VCF AD format field by counts from BAM files
  • Run MCHap software to build haplotypes based on GATK called markers
  • Include or not multiallelic (MNP) markers
  • Apply filters using VCFtools

This workflow requires:

  • Diploid bi-parental F1 population
  • Single-end reads
  • A reference genome
  • Genomic positions for markers order
  • Selection of a single chromosome from a reference genome to build the linkage maps
Assets 5
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