5.11 PSMC

Generating a PSMC Input file probabilistically

PSMC generates an input file for PSMC (pairwise sequentially Markovian coalescent). This task takes an input bam file, where the possible letters are T=Homozygous, K=Heterozygous, N=unknown. Each letter represents a window of 100bp of a genome, and windows with zero heterozygous sites is defined as a “T” and windows with at least 1 heterozygous site as a “K”. In order for ATLAS to be able to produce such a file, two further things need to be defined:a prior on theta, which is the heterozygosity you expect to see a priori, and a confidence threshold. For each window, ATLAS calculates the posterior probability of it being a “K” or a “T”. If neither of these probabilities is higher than the confidence threshold, the window is defined as an “N”.

5.11.1 Parameters

5.11.1.1 Input

--bam Input_bam_file.bam Input bam file.

5.11.1.2 Specific

Parameter Description Default
--theta value Prior for heterozygosity. 0.001
--confidence value Confidence threshold for assigning a window with a “T” or a “K”. 0.99
--window value Windows must be at least as large as the max read length. 100000bp
--minMAF value Keep only sites for which minor allele frequency is at the least the indicated number. keep all

5.11.2 Output

*.psmcfa PSMC input file.

5.11.3 Usage Example

# Simulate a BAM File
atlas simulate

# Generating a PSMC Input file
atlas PSMC --bam ATLAS_simulations.bam