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Variant Calling Pipeline
By LEGE 64 days ago
https://github.com/Tom-Jenkins/nextflow-pipelines/blob/main/docs/variant-calling.md
The variantcalling.nf nextflow script will take any number of samples with paired-end reads in FASTQ format, map reads using Bowtie2, process BAM files, and finally call variants using BCFtools v1.21 and/or Freebayes v1.3.6. If part of the pipeline is unsuccessful for a sample then these errors are ignored.
Pipeline flowchart:
