Supplemental Material for Maruki and Lynch, 2017
Files in this Data Supplement:
- File S2 - Documentation of the updated genotype-frequency estimator. (.pdf, 85 KB)
- Table S4 - Summary of the realized parameter values in population samples in simulated diploid data at biallelic sites. (.pdf, 108 KB)
- Table S5 - Summary of the realized parameter values in population samples in simulated diploid data at triallelic sites. (.pdf, 84 KB)
- Table S6 - Comparison of the performance of the triploid genotype caller to that of GATK. (.pdf, 107 KB)
- File S4 - Documentation of the Bayesian genotype caller. (.pdf, 79 KB)
- File S6 - Documentation of the high-coverage genotype caller. (.pdf, 80 KB)
- File S8 - Documentation of the triploid genotype caller. (.pdf, 80 KB)
- File S10 - Documentation of the tetraploid genotype caller. (.pdf, 80 KB)
- File S12 - Documentation of the C++ program for removing multiallelic sites identified by HGC. (.pdf, 80 KB)
- Table S1 - Probability of an observed nucleotide read as a function of the individual genotype g and error rate ε in the triploid sequence data. (.pdf, 143 KB)
- Table S2 - Probability of an observed nucleotide read as a function of the individual genotype g and error rate ε in the tetraploid sequence data. (.pdf, 151 KB)
- Table S3 - Comparison of the allele-frequency estimates and called genotypes by different methods with moderately high depths of coverage. (.pdf, 121 KB)
- File S1 - C++ program of the updated genotype-frequency estimator (GFE_v2.0.cpp). (.zip, 6 KB)
- File S3 - C++ program of the Bayesian genotype caller (BGC.cpp). (.zip, 4 KB)
- File S5 - C++ program of the high-coverage genotype caller (HGC.cpp). (.zip, 8 KB)
- File S7 - C++ program of the triploid genotype caller (TRI.cpp). (.zip, 11 KB)
- File S9 - C++ program of the tetraploid genotype caller (TET.cpp). (.zip, 14 KB)
- File S11 - C++ program for removing multiallelic sites identified by HGC (Rem_Multi_Allelic.cpp). (.zip, 2 KB)