ciscall validate-env

$ ciscall validate-env
  • Validate the software requirements of cisCall.

ciscall download-asset

$ ciscall download-assset --dest-dir <output directory>
  • Download input data files used by ciscall run.
    • The files are based on hg19.

ciscall merge-snp

  • This command is under development.
  • Merge SNP files from multiple sources into a single VCF file.

ciscall prepare-ref

  • This command is under development.
  • Prepare reference files for variant calling.

ciscall run

$ ciscall run \
    --fg-r1-fastq <foreground_read1_fastq_gz> \
    --fg-r2-fastq <foreground_read2_fastq_gz> \
    --bg-r1-fastq <background_read1_fastq_gz> \
    --bg-r2-fastq <background_read2_fastq_gz> \
    --target-bed <target_bed> \
    --fusion-bed <fusion_bed> \
    --genome-fa <genome_fa> \
    --refgene-txt <refgene_txt> \
    --snp-vcf <snp_vcf_gz> \
    --mapability-bigwig <bigwig> \
    --gene-bed <gene_bed> \
    --fusion-gene-txt <gene_pair_txt> \
    --gene-family-txt <genefamilies_txt> \
    --decoy-fa <decoy_fa>