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README_13_remove_snps_different_means.md

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Remove SNPs with different means

The MergeGenome remove-snps-different-means command removes all the common markers (i.e., SNPs at the same CHROM, POS, REF, and ALT) between a query and reference datasets that have a mean absolute difference higher than a threshold (by default, 0.1). It is a fast solution to identifying and removing outlier SNPs, which might harm any analysis built on top of corrupt features. The query and reference with the filtered SNPs are stored in a new VCF file.

The provided .vcf files must contain data for the same single chromosome, and the files need to appear in the same chromosomical order.

Usage

$ python3 MergeGenome.py remove-snps-different-means -q <query_file_1>...<query_file_n> -r <reference_file_1>...<reference_file_n> -o <output_folder>

Input flags include:

  • -q, --query LIST, Path to query .vcf files with data for for a single chromosome each (required).
  • -r, --reference LIST, Paths to reference .vcf files with data for for a single chromosome each (required).
  • -o, --output-folder PATH, Path to output folder (required). Note: make sure a '/' appears at the end of the output folder.
  • -t, --threshold FLOAT, All common SNPs with a mean absolute difference higher than this threshold will be removed (optional). Accepted values are between 0.0 and 1.0. Default=0.1.
  • -d, --debug PATH, Path to .log/.txt file to store info/debug messages (optional).

Output

  • One .vcf file with filtered data for each input query and reference files. Each new .vcf file will receive the same base name as the input file, but ending with '_removed.vcf'.
  • If --debug, a .log or .txt file with information regarding the dimensions of the data (number of samples and number of SNPs), the chromosome in each file, and the amount SNPs removed.

Example

  1. Remove all the common SNPs with a mean absolute difference higher than 0.2:
$ python3 MergeGenome.py remove-snps-different-means -q query_chr1.vcf -r reference_chr1.vcf -o ./output/ -t 0.2