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
• The filtered reads are aligned with bwa-mem.
• Only properly aligned mate pairs are retained, PCR duplicates are removed.
• Alignments are re-aligned using lofreq viterbi and variants are called with lofreq call.
• Variants are annotated with snpeff eff