Nextflow DNA somatic mutation detector pipeline for MIPS AML samples sequenced using Illumina NextSeq.
Clone the directory using git clone Enter the directory and create a new directory for your run sequences (R1 and R2). For example, sequences_10Dec2021 Ensure all fastqs of appropriate size and both R1 and R2 are present Modify the samplelist.csv i.e. choosing 8-10 samples as per priority and save.
Make changes in the run_nextflow.sh with respect to -entry [MIPS] --bedfile [Your bedfile without .bed extension] --sequences of sequences [Samples path]
Run the run_nextflow.sh file using cluster or directly