flobenhsj/quantisnp_penncnv repository overview

### ⚠️ This is an example — paths refer to files INSIDE the QuantiSNP Docker image

# Chromosomes to analyse:
chr="1:23"

# Sample biological sex (used for chrX correction):
gender="male"   # or "female"

# QuantiSNP parameter and model files
config="/usr/local/QuantiSNP-2.3/bin/config/params.dat"
levels="/usr/local/QuantiSNP-2.3/bin/config/levels.dat"

# GC correction directory (genome_version = GRCh38 or GRCh37)
gcdir="/usr/local/QuantiSNP-2.3/GC_correction/${genome_version}/GCdir/"


quantisnp \
  --chr "${chr}" \
  --outdir . \
  --sampleid <sample_id> \             # unique sample identifier (string)
  --gender "${gender}" \               # male or female
  --config "${config}" \               # params.dat
  --levels "${levels}" \               # levels.dat
  --gcdir "${gcdir}" \                 # GC correction directory
  --input-files <path/to/input.tsv> \  # tab-separated SNP file (LRR + BAF)
  --doXcorrect \                       # enable X-chromosome correction
  --verbose &> <sample_id>.quanti.log  # redirect stdout+stderr to log

# HMM files are available inside the container at:
#   /usr/local/PennCNV-1.0.5/lib/
#     - hhall.hmm  -> general high-density SNP arrays
#     - hh550.hmm  -> Illumina HumanHap550-specific
#     - wgs.hmm    -> whole-genome sequencing

```bash
penncnv --test \
  --pfbfile pfbfile.pfb \
  --hmmfile <path/to/hmmfile> \
  --logfile <sample_id>.pcnv.chrx.log \
  --minlength <minlength> \
  --minconf <minconf> \
  --output <sample_id>.pcnv.chrx.out \
  --gcmodelfile <path/to/gcmodelfile.txt> \
  --sexfile <path/to/sexfile.tsv> \
  --chrx \
  <path/to/tsv_input_file>