vcf2bayescan.spid

# spid-file generated: Wed Mar 02 17:43:34 CST 2022

# VCF Parser questions
PARSER_FORMAT=VCF

# Only output SNPs with a phred-scaled quality of at least:
VCF_PARSER_QUAL_QUESTION=
# Select population definition file:
VCF_PARSER_POP_FILE_QUESTION=/home/cbird/Projects/PuntioplitesFalcifer/mkBAM2/popmap.3.7
# What is the ploidy of the data?
VCF_PARSER_PLOIDY_QUESTION=DIPLOID
# Do you want to include a file with population definitions?
VCF_PARSER_POP_QUESTION=true
# Output genotypes as missing if the phred-scale genotype quality is below:
VCF_PARSER_GTQUAL_QUESTION=
# Do you want to include non-polymorphic SNPs?
VCF_PARSER_MONOMORPHIC_QUESTION=false
# Only output following individuals (ind1, ind2, ind4, ...):
VCF_PARSER_IND_QUESTION=
# Only input following regions (refSeqName:start:end, multiple regions: whitespace separated):
VCF_PARSER_REGION_QUESTION=
# Output genotypes as missing if the read depth of a position for the sample is below:
VCF_PARSER_READ_QUESTION=
# Take most likely genotype if "PL" or "GL" is given in the genotype field?
VCF_PARSER_PL_QUESTION=false
# Do you want to exclude loci with only missing data?
VCF_PARSER_EXC_MISSING_LOCI_QUESTION=false

# GESTE / BayeScan Writer questions
WRITER_FORMAT=GESTE_BAYE_SCAN

# Specify which data type should be included in the GESTE / BayeScan file  (GESTE / BayeScan can only analyze one data type per file):
GESTE_BAYE_SCAN_WRITER_DATA_TYPE_QUESTION=SNP