<filename>cnvlib/params.py
"""Hard-coded parameters for CNVkit. These should not change between runs."""
# Filter thresholds used in constructing the reference (log2 scale)
MIN_REF_COVERAGE = -5.0
MAX_REF_SPREAD = 1.0
NULL_LOG2_COVERAGE = -20.0

# Fragment size for paired-end reads
INSERT_SIZE = 250

# Target/bin names that are not meaningful gene names
# (In some UCSF panels, "CGH" probes denote selected intergenic regions)
IGNORE_GENE_NAMES = ("-", ".", "CGH")
ANTITARGET_NAME = "Antitarget"
ANTITARGET_ALIASES = (ANTITARGET_NAME, "Background")

<filename>cnvlib/params.py
"""Hard-coded parameters for CNVkit. These should not change between runs."""
# Filter thresholds used in constructing the reference (log2 scale)
MIN_REF_COVERAGE = -5.0
MAX_REF_SPREAD = 1.0
NULL_LOG2_COVERAGE = -20.0

# Fragment size for paired-end reads
INSERT_SIZE = 250

# Target/bin names that are not meaningful gene names
# (In some UCSF panels, "CGH" probes denote selected intergenic regions)
IGNORE_GENE_NAMES = ("-", ".", "CGH")
ANTITARGET_NAME = "Antitarget"
ANTITARGET_ALIASES = (ANTITARGET_NAME, "Background")

Hard-coded parameters for CNVkit. These should not change between runs. # Filter thresholds used in constructing the reference (log2 scale) # Fragment size for paired-end reads # Target/bin names that are not meaningful gene names # (In some UCSF panels, "CGH" probes denote selected intergenic regions)