Principle Components Analysis

NGS PopGen PCA calculation. See NGSPopGen for full details on this method.

To use this method, you would run:

bash ./scripts/PCA.sh ./scripts/PCA.conf

with the proper taxon name filled in the configuration file.

Input files

Scripts

• scripts/PCA.sh
• scripts/PCA_TAXON.conf

Necessary input files

• data/TAXON_samples.txt bam list

Output files

• results/TAXON_test_PCA.covar (file to graph)
• results/TAXON_test_PCA.geno

Mandatory PCA.conf Variables

• TAXON

Optional PCA.conf Variables

• UNIQUE_ONLY uniquely mapped reads (default=0)
• MIN_BASEQUAL minimum base quality (default=20)
• BAQ adjust qscores around indels (as SAMtools) (default=1)
• MIN_IND minimum number of individuals needed to use site (default=1)
• MIN_MAPQ minimum base mapping quality to use (default=30)
• N_CORES number of cores to use (default=32)
• DO_COUNTS count bases at each site after filtering (default=1)
• DO_ABBABABA sample a random base at each position (default=1)
• CHECK_BAM_HEADERS check bam headers (default=0)
• BLOCKSIZE size of each block. choose a number higher than LD in the populations (default=1000)