Nextflow pipeline to detect matched BAMs with NGSCheckMate.

Implementation of NGSCheckMate and its underlying subset calling, distibuted per sample.

1. This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
2. NGSCheckMate (follow instructions, especially setting up $NCM_HOME variable)
3. samtools
4. bcftools

• --input : your input BAM file(s) (do not forget the quotes e.g. --input "test_*.bam")
• --output_dir : the folder that will contain NGSCheckMate folder with all results in text files.
• --ref_fasta : your reference in FASTA.
• --bed : Panel of SNP bed file from NGSCheckMate.

A nextflow.config is also included, please modify it for suitability outside our pre-configured clusters (see Nexflow configuration).

nextflow run iarcbioinfo/NGSCheckMate.nf -profile cobalt --input "/data/test_*.bam" --output_dir /data/cohort_output --ref_fasta /ref/Homo_sapiens_assembly38.fasta --bed /home/user/bin/NGSCheckMate/SNP/SNP_GRCh38.bed