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configuration_example_2_of_2.ini
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configuration_example_2_of_2.ini
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# 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".
[12]
# ##############################################################################
# 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. Note that
# the two options 'reason-marker' and 'reason-sample' are for the automatic
# report generated after the analysis.
# ##############################################################################
script = subset
reason-marker = reason for marker exclusion
reason-sample = reason for sample exclusion
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
[13]
# ##############################################################################
# Removes heterozygous haploid genotypes from the dataset.
# ##############################################################################
script = remove_heterozygous_haploid
[14]
# ##############################################################################
# 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
[15]
# ##############################################################################
# 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