diff --git a/workflows/variant-calling/haploid-variant-calling-wgs-pe/README.md b/workflows/variant-calling/haploid-variant-calling-wgs-pe/README.md index 0aabda928..12ff08b33 100644 --- a/workflows/variant-calling/haploid-variant-calling-wgs-pe/README.md +++ b/workflows/variant-calling/haploid-variant-calling-wgs-pe/README.md @@ -1,11 +1,18 @@ # Haploid variant calling for whole genome sequencing paired end data +This workflow uses Illumina or Element read data to discover variants (short nucleotide polymorphisms, SNPs, and small indels) in haploid genomes with multiple genomic sequences (contigs, scaffolds, or chromosomes). + ## Inputs dataset - The workflow needs a list of paired end fastq files - A GTF containtaing the Gene annotation for the selected haploid genome - A fasta file for the haploid genome to call variants against +## Outputs + +- Tab-delimited summary of annotated variants +- Report summarizing the quality of input data and mapping results + ## Processing - The workflow will remove adapters using fastp