MIPS pipeline

Description

This is a nextflow pipeline for analysing data for MIPS-MRD. It follows the fgbio pipeline (https://github.com/fulcrumgenomics/fgbio) to obtain mapped consensus bam file.

For running this pipeline, following programs need to be installed and their complete paths need to be added in the params section of the nextflow.config.

• fastqc = fastqc executable path
• java_path = directory containing the java executable
• GATK38_path = path to the GenomeAnalysisTK-3.8.jar file
• GATK42_path = path to the gatk-package-4.2.6.0-local.jar file
• fgbio_path = ath to the fgbio-2.0.1.jar file
• samtools = samtools executable path
• genome = Genomic fasta file
• site1 = known_polymorphic_sites 1 (Mills_and_1000G_gold_standard.indels)
• PosControlScript = Custom script for generating Synthetic Fastq with 4% npm1 VAF
• fastq_bam = Custom script for generating bam from fastq with bwa
• abra2_path = directory containing the abra jar file
• pear_path = pear executable path
• bedtools = bedtools executable path
• mosdepth
• picard_path = path to the picard.jar file
• get_itd_path = path to the folder containing getitd.py
• VarDict
• varscan_path = path to the VarScan.v2.3.9.jar file
• annovarLatest_path = path to the folder containing ANNOVAT perl scripts
• bcftools_path = bcftools executable path
• somaticseq

Usage:

1. Keep the fastq files into the sequences/ folder.

2. Change the samplesheet.csv. It should have a list of IDs of the samples.

3. Run the following script.

./run_nextflow.sh > script.log

This script contains the nextflow command used to execute the workflow.

source activate new_base

nextflow -c /home/pipelines/Consensus_pipeline_with_espresso/nextflow.config run mips_mrd.nf -entry MRD \
--bedfile /home/pipelines/Consensus_pipeline_with_espresso/bedfiles/mips_mrd_bal210125_sortd \
--bedfile2 /home/pipelines/Consensus_pipeline_with_espresso/bedfiles/mips_mrd_bal11March_exon_sortd \
--sequences /home/pipelines/Consensus_pipeline_with_espresso/sequences/ \
--input /home/pipelines/Consensus_pipeline_with_espresso/samplesheet.csv \
-resume -bg

conda deactivate