Duplicated Markers Module¶

The usage of the standalone module is shown below:

\$ pyGenClean_duplicated_snps --help
usage: pyGenClean_duplicated_snps [-h] [-v] --tfile FILE
[--snp-completion-threshold FLOAT]
[--snp-concordance-threshold FLOAT]
[--frequency_difference FLOAT] [--out FILE]

Extracts and merges duplicated markers.

optional arguments:
-h, --help            show this help message and exit
-v, --version         show program's version number and exit

Input File:
--tfile FILE          The input file prefix (will find the tped and tfam
file by appending the prefix to .tped and .tfam,
respectively. A .map file is also required.

Options:
--snp-completion-threshold FLOAT
The completion threshold to consider a replicate when
choosing the best replicates and for composite
creation. [default: 0.9]
--snp-concordance-threshold FLOAT
The concordance threshold to consider a replicate when
choosing the best replicates and for composite
creation. [default: 0.98]
--frequency_difference FLOAT
The maximum difference in frequency between duplicated
markers [default: 0.05]

Output File:
--out FILE            The prefix of the output files. [default: dup_snps]


Input Files¶

This module uses PLINK’s transposed pedfile format (tped and tfam files). It also requires a map file to speed up the process of finding the duplicated markers, so that the tped file is not read.

Procedure¶

Here are the steps performed by the module:

1. Reads the map file to gather marker’s position.
2. Reads the tfam file.
3. Finds the unique markers using the map file.
4. Process the tped file, finding unique and duplicated markers according to chromosomal positions.
5. If there are no duplicated markers, stop here.
6. If there are duplicated markers, print a tped and tfam file containing the duplicated markers.
7. Computes the frequency of the duplicated markers (using Plink) and read the output file.
8. Computes the concordance and pairwise completion of each of the duplicated markers.
9. Prints the problematic duplicated markers with a file containing the summary of the statistics (completion and pairwise concordance).
10. Print the pairwise concordance in a file (matrices).
11. Choose the best duplicated markers using concordance and completion.
12. Completes the chosen markers with the remaining duplicated markers.
13. Creates the final tped file, containing the unique markers, the chosen duplicated markers that were completed, and the problematic duplicated markers (for further analysis). This set excludes markers that were used for completing the chosen ones.

Output Files¶

The output files of each of the steps described above are as follow (note that the output prefix shown is the one by default [i.e. dup_snps]):

1. If the marker names are not unique, one file is created:
• dup_snps.duplicated_marker_names: a list of marker names and chromosomal positions for each marker with duplicated names. This file is not created if there are no markers with duplicated names.
2. No files are created.
3. No files are created.
4. One set of transposed pedfiles.
• dup_snps.unique_snps: the transposed pedfiles containing the unique markers (according to chromosomal positions).
5. If there are no duplicated markers (according to chromosomal positions), the transposed pedfiles created at the previous step are copied to a new set of transposed pedfiles.
• dup_snps.final: the final transposed pedfiles.
6. One set of transposed pedfiles.
• dup_snps.duplicated_snps: the transposed pedfiles containing the duplicated markers (according to chromosomal positions).
7. One set of PLINK’s result file.
• dup_snps.duplicated_snps: the file with the frq extension contains the frequency of each duplicated markers.
8. No files are created.
9. Multiple files are created.
• dup_snps.summary: contains the completion and pairwise concordance between duplicated markers.
• dup_snps.problems: contains the list of markers with “problems” that can’t be used for further completion of the duplicated markers. (either a difference in MAF [diff_frequency], a difference in the minor allele [diff_minor_allele], two homozygous markers where one is flipped [homo_flip], markers with flipped alleles [flip], one marker is homozygous, the other is heterozygous [homo_hetero], one marker is homozygous, the other is heterozygous but one is flipped [homo_hetero_flip] or any other problem [problem].
10. One output file is created.
• dup_snps.concordance: a matrix containing a pairwise concordance comparison for each duplicated markers.
11. Two output files are created.
• dup_snps.chosen_snps.info: the list of duplicated markers that were chosen for completion with the other markers (the best of the duplicated markers, according to concordance and completion).
• dup_snps.not_chosen_snps.info: the list of duplicated markers that were not chosen for completion with the other markers.
12. Multiple output files are created along with a set of transposed pedfiles.
• dup_snps.zeroed_out: the list of genotypes that were zeroed out while completing the chosen duplicated markers with the others. Each line contains the id of the sample and the name of the marker that was zeroed out.
• dup_snps.not_good_enough: the list of markers that were not good enough (according to concordance and completion) to complete the best of the duplicated markers.
• dup_snps.removed_duplicates: the list of markers that were used to complete the chosen duplicated markers. Those markers were removed from the dataset.
• dup_snps.chosen_snps: the transposed pedfiles containing the completed chosen duplicated markers (a composite of all the duplicated markers that were good enough).
13. On set of transposed pedfiles.
• dup_snps.final: the final dataset, containing the unique markers, the chosen duplicated markers that were complete (composite) and the duplicated markers that weren’t completed because of various problems.