# This is the second part of example configuration files for performing
# efficient data clean up. All commented out parameters are those that are used
# by default.

# The input file should be the output file of the second sample missigness step
# (which is the one that has been used by any of these scripts):
#    - sex_check
#    - find_related_samples
#    - check_ethnicity
#    - plate_bias

# Note that the final usable dataset is the one located in the directory where
# "remove_heterozygous_haploid" was run (which is the one that has been used by
# any of these scripts):
#    - flag_maf_zero
#    - flag_hw
# Hence, if you want to remove the flagged markers, you should use
# pyGenClean_subset_data on markers in the "flag_maf_zero" and "flag_hw"
# directories using the PLINK's binary file located in
# "remove_heterozygous_haploid".

[11]
# ##############################################################################
# After manually checking that everything went fine in the previous steps, you
# need to create a list of samples to remove from steps [7] to [10] and a list
# of markers to exclude from steps [6]. Just create a file containing family and
# individual identification numbers for all those samples to remove.
# ##############################################################################

script = subset
remove = /PATH/TO/FILE/CONTAINING/ALL_SAMPLES_FROM_PREVIOUS_STEPS_TO_REMOVE.txt
exclude = /PATH/TO/FILE/CONTAINING/ALL_MARKERS_FROM_PREVIOUS_STEPS_TO_EXCLUDE.txt



[12]
# ##############################################################################
# Removes heterozygous haploid genotypes from the dataset.
# ##############################################################################

script = remove_heterozygous_haploid



[13]
# ##############################################################################
# Flags uninformative markers (with a MAF of 0). This step only flag markers.
# You might want to exclude them later on.
# ##############################################################################

script = flag_maf_zero



[14]
# ##############################################################################
# Flags markers that fail HWE test for a p value of 1e-4 and after Bonferroni
# correction. This step only flag markers. You might want to exclude them later
# on.
# ##############################################################################

script = flag_hw
# hwe = 1e-4