Aim:
Identify sequence variants using the outputs from the “ONTprocessing” pipeline. NextFlow: ONTprocessing pipeline. Generated minimap2 alignments are processed using https://github.com/kishwarshafin/pepper to identify highly reliable sequence variants (i.e., SNPs).
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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:
| Code Block |
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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 |