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EmpiricalSNPCalling_v1.0.0
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@Cristianetaniguti Cristianetaniguti released this 25 Nov 19:10
· 215 commits to main since this release
EmpiricalSNPCalling_v1.0.0
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Learn about vigilant mode.

1.0.0

Initial release

This workflow performs the alignment of FASTQ to a reference genome, SNP calling with GATK tools (HaplotypeCaller, GenomicsDBImport, and GenotypeGVCFs) and Freebayes. The 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 also include de options to:

  • Remove of 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

This workflow requires:

  • Diploid or polyploid specie
  • Single-end reads
Assets 5
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