Aim:
Identify sequence variants using the outputs from the NextFlow: ONTprocessing pipeline. Generated minimap2 alignments are processed using https://github.com/kishwarshafin/pepper to identify highly reliable sequence variants (i.e., SNPs).
Preparing a samplesheet.csv file
The nextflow ‘eresearch/deepvariant’ pipeline requires a sample metadata file that specifies: sample ID, BAM alignment, BAI index, and genome reference. For example:
sampleid,sample_files,sample_files_index,reference NC483,/ontprocessing/NC483/run1/results/samtools/NC483_aln.sorted.bam,/ontprocessing/NC483/run1/results/samtools/NC483_aln.sorted.bam.bai,/data/ref/NC483_NC001477_reference_sequence.fasta