G'day all,
I am trying to convert a vcf file to a genepop file using PGDSpider command line. I want to include a population file so that my new genepop file has this information included.
I created the .spid file in the GUI because I couldn't figure out how to do this in linux. The .spid file points to the incorrect location for the popfile because when I was making the .spid file I had to specify a popfile which was on my regular computer not in my linux virtual machine directory.
I moved the popfile to my linux machine and change the .spid file so that it pointed to the correct location of the popfile, but I still get an error saying it can't find my popfile. Has anyone else had this problem and know how to fix it?
The .spid file is below, with my change to the path directory for the popfile. Does it look right or have I done something wrong, e.g. not specified the full path?
Thanks for your help.
Cheers,
Adam
# spid-file generated: Fri Aug 01 10:56:50 EST 2014
# VCF Parser questions
PARSER_FORMAT=VCF
# Do you want to include a file with population definitions?
VCF_PARSER_POP_QUESTION=true
# Only input following regions (refSeqName:start:end, multiple regions: whitespace separated):
VCF_PARSER_REGION_QUESTION=
# What is the ploidy of the data?
VCF_PARSER_PLOIDY_QUESTION=DIPLOID
# Only output following individuals (ind1, ind2, ind4, ...):
VCF_PARSER_IND_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
# Select population definition file:
VCF_PARSER_POP_FILE_QUESTION=/home/apcar/starling_gbs/pops/spid_10_20_10_popfile.txt
# Only output SNPs with a phred-scaled quality of at least:
VCF_PARSER_QUAL_QUESTION=
# Do you want to include non-polymorphic SNPs?
VCF_PARSER_MONOMORPHIC_QUESTION=false
# Output genotypes as missing if the phred-scale genotype quality is below:
VCF_PARSER_GTQUAL_QUESTION=
# STRUCTURE Writer questions
WRITER_FORMAT=STRUCTURE
# Save more specific fastSTRUCTURE format?
STRUCTURE_WRITER_FAST_FORMAT_QUESTION=false
# Specify the locus/locus combination you want to write to the STRUCTURE file:
STRUCTURE_WRITER_LOCUS_COMBINATION_QUESTION=
# Specify which data type should be included in the STRUCTURE file (STRUCTURE can only analyze one data type per file):
STRUCTURE_WRITER_DATA_TYPE_QUESTION=SNP
# Do you want to include inter-marker distances?
STRUCTURE_WRITER_LOCI_DISTANCE_QUESTION=false
