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analysis.yaml
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analysis.yaml
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# run SV calling (0) or vanilla jobs (1)
echo_run: 1
# select one or more callers
enable_callers:
- manta
- delly
- lumpy
- gridss
# (s)ingle-sample or (p)aired-samples analysis
mode: p
# filepath of the reference genome in FASTA format
genome: data/fasta/chr22.fasta
# filepath of the exclusion list in BED format
exclusion_list: data/ENCFF001TDO.bed
exclude_regions: 1 # use the list (1) or don't (0)
# file extensions used by the workflow
file_exts:
fasta: .fasta
fasta_idx:
- .fasta.fai # faidx index file
- .fasta.bwt # BWA v0.6.x index files
- .fasta.amb # |
- .fasta.ann # |
- .fasta.pac # |
- .fasta.sa # |
bam: .bam
bam_idx: .bam.bai
vcf: .vcf
bcf: .bcf
bed: .bed
# CSV file with (paired) WGS samples for analysis
# format: PATH,SAMPLE1,SAMPLE2
# paired SAMPLE1(tumor)/SAMPLE2(normal) files used for somatic analysis while
# single SAMPLE1 file used for germline or tumor-only analysis (Manta only)
samples: samples.csv
# settings or requirements per SV caller
callers:
manta:
threads: 24 # number of threads used
memory: 16384 # allocated memory (MB)
tmpspace: 0 # min. temporary disk space (MB); not in use by Manta
outdir: manta_out # output dir relative to PATH/SAMPLE/... (see above)
tumor_only: 0 # germline (0) or tumor-only analysis (1)
delly:
threads: 2 # max. 2 for paired-samples otherwise defaults to 1
memory: 8192
tmpspace: 0 # not in use
outdir: delly_out
sv_types:
- BND # translocation
- DEL # deletion
- DUP # duplication
- INS # insertion
- INV # inversion
lumpy:
threads: 1 # multi-threading not supported
memory: 32768
tmpspace: 0 # e.g., 10240
outdir: lumpy_out
gridss:
threads: 24
memory: 63488
tmpspace: 0 # e.g., 102400
outdir: gridss_out
postproc:
survivor:
threads: 1
memory: 1024
tmpspace: 0 # not in use
outdir: survivor
filter: # filter SVs using a BED file (see 'exclusion_list')
min_size: -1 # min. SV size (-1 to disable)
max_size: -1 # max. SV size (-1 to disable)
min_freq: 0 # min. allele frequency (0 or 1)
min_sup: -1 # min. number of reads support: RE flag (-1 to disable)
merge: # merge callers' output into one (union) SV set
infile: all.txt # list of VCF files
max_dist: 100 # max. distance (bp) between breakpoints
min_sup: 1 # min. number of supporting callers
use_type: 0 # take SV type into account (1=yes or 0=no)
use_strand: 0 # take the strands of SVs into account (1=yes or 0=no)
use_size: 0 # estimate distance based on SV size (1=yes or 0=no)
min_size: 0 # min. SV size (bp)
outfile: all.vcf