CueSea

INTRODUCTION

This tool is designed for quality control of Illumina microarrays genotyping data.

PREREQUISITES

To run this tool on your machine, you need to have Python 2.7 or 3 installed. Besides that, you need several packages, which can be installed using pip. -scikit-learn -plotly

HOW TO RUN

1. Most common scenario: python3 cuesea.py Genome_Studio_Report.txt --snps=snps.txt This command will run QC using your Genome_Studio_Report.txt as data file and snps.txt as list of snps to analyze. X and Y chromosome snps treated as autosomal.
2. Gender python3 cuesea.py Genome_Studio_Report.txt --snps=snps.txt --gender gender.txt This command will run QC using your Genome_Studio_Report.txt as data file and snps.txt as list of snps to analyze. This will include proper analyze of X and Y chromosome snps as described in HOW IT WORKS paragraph.
3. Angle python3 cuesea.py Genome_Studio_Report.txt --angle 8.0 The --angle key specifies max angle between points of each cluster. The default value is 8.0 degrees, but you can slightly increase or dicrease it.

INPUT FILE FORMATS

1. Genome Studio Report This tool uses default Genome Studio report, and we use columns:

• SNP Name (which is Illumina Name)
• Sample ID
• Allele 1 - Top
• Allele 2 - Top
• Chr
• X
• Y

2. Snps list List of snps, one per line.
3. Gender File with two tab-separated columns (Sample ID, gender) no header. F - for women, M - for men. Other symbols treated as undefined gender. For example: 0000-1111 F

OUTPUT FILES

Tool outputs 3 types of reports:

1. Sample Report - list of snps, which have not pass the QC. This file contains columns: SNP - Sample ID - error code. Error code 0 - snp fails intensity check Error code 1 - snp failed clusterization step Error code 2 - snp failed gender check Error code 3 - snp’s genotype distribution doesn’t fit to HWE
2. Overall report - list of snps with statistics. This file contains columns: SNP - Number of samples - Excluded by QC - Excluded by R(intensity) - Excluded by clusterization Or if it was gender file on input: SNP - № of samples - Excluded by QC - Excluded by R(intensity) - Excluded by clusterization - Excluded from X\Y
3. Genotype Report - information about SNPs with changed genotype class This file contains columns: SNP - Sample ID - old GT class - new GT class
4. Plots Samples marked green - passes QC Samples marked blue - not passed QC Samples marked red - changed GT class

AUTHORS

Daria Iakovishina, PhD

Nikita Moshkov

LICENSE

GNU GPL v.3