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Parameters
This is a list of all possible parameters for various methods in ANGSD-wrapper
Calculate base alignment quality
Possible value | Meaning |
---|---|
0 | Do not calculate BAQ score |
1 | Standard BAQ score |
2 | Extended BAQ score |
Set the size for each block
Any integer higher than the linkage disequilibrium
Perform genotype calling
Possible value | Meaning |
---|---|
0 | Do not call genotypes |
1 | Call genotypes |
Perform Abbababa analysis
Possible value | Meaning |
---|---|
1 | Perform Abbababa |
Count allele frequencies
Possible value | Meaning |
---|---|
0 | Do not count allele frequencies |
1 | Count allele frequencies |
Extract FASTA sequence from BAM file
Possible value | Meaning |
---|---|
0 | Do not extract FASTA sequence |
1 | Extract FASTA sequence by sampling random base at each position |
2 | Use the most common base |
3 | Use base with highest effective depth |
Call genotypes from genotype likelihoods
Possible value | Meaning |
---|---|
1 | Print in major-minor format |
2 | Print in -1, 0, 1, 2 format |
4 | Print in allele format |
8 | Print all three posteriors |
16 | Print posterior of called genotype |
32 | Binary posterior |
Note: These values can be summed to combine output types |
Output genotype likelihood frequency file
Possible value | Meaning |
---|---|
1 | Binary file with log 10 likelihoods |
2 | Beagle file |
3 | Beagle binary file |
4 | Flat text file with log 10 likelihoods |
Calculate allele frequencies
Possible value | Meaning |
---|---|
0 | Calculate per-site frequencies |
1 | Frequency with fixed major and minor alleles |
2 | Frequency, with fixed major alleles and unknown minor alleles |
4 | Frequency from genotype probabilities |
8 | AlleleCounts-based methods using known major and minor alleles |
NB | Suppress file dumping if frequency is negative |
- Fst Estimations
- Genotype Likelihoods
- Inbreeding Coefficients
- Principle Component Analysis
- Site Frequency Spectrum
- Thetas Estimation
Determine major and minor alleles
Possible value | Meaning |
---|---|
1 | Infer major and minor from genotype likelihoods |
2 | Infer major and minor from allele counts |
4 | Use reference allele as major |
5 | Use ancestral allele as major |
- Genotype Likelihoods
- Inbreeding Coefficients
- Principle Component Analysis
- Site Frequency Spectrum
- Thetas Estimation
Calculate the posterior probability
Possible value | Meaning |
---|---|
0 | Calculate posterior probability from genotype probabilities |
1 | Use the per-site frequency as a prior |
2 | Use a uniform prior |
Generate site allele frequencies
Possible value | Meaning |
---|---|
1 | Calculate site allele frequencies assuming Hardy–Weinberg Equilibrium |
2 | Take inbreeding coefficients into account |
3 | Use site frequency spectrum as prior distribution |
4 | Use genotype probabilities as prior information |
Calculate genotype likelihoods
Possible value | Meaning |
---|---|
1 | Use SAMTools model for genotype likelihoods |
2 | Use GATK model |
3 | Use SOAPsnp model |
4 | Use SYK model |
- Genotype Likelihoods
- Inbreeding Coefficients
- Principle Component Analysis
- Site Frequency Spectrum
- Thetas Estimation
Calculate global Fst values
Possible value | Meaning |
---|---|
true |
Calculate global Fst values |
false |
Do not calculate global Fst values |
Set the number of assumed populations to estimate Admixture under
Any integer greater than or equal to 2
Set the minimum base quality
Any positive integer
Set the minimum root-mean-square deviation between to assume convergence
Any positive floating point value
Set the minimum number of individuals required
Any positive integer
Note: Fst Estimations have two MIN_IND
fields, one for each population
Set the minimum minor allele frequency
Any positive floating point value
Set the minimum mapping quality for a base to be used
Any positive integer
Set the number of threads and cores to be used by ANGSD-wrapper
Any positive integer less than or equal to the number of CPU cores on your system
- Abbababa
- Admixture Analysis
- Genotype Likelihoods
- Inbreeding Coefficients
- Principle Component Analysis
- Site Frequency Spectrum
- Thetas Estimation
Set the maximum number of sites to use for Principal Component Analysis
Any positive integer
Normalize by allele frequency
Possible value | Meaning |
---|---|
0 | Do not normalize by allele frequency |
1 | Normalize by allele frequency |
Overwrite any previously generated results
Possible value | Meaning |
---|---|
true |
Overwrite previous results |
false |
Do not overwrite previous results |
Set the minimum posterior value for calling genotypes
Any positive floating point value
Remove transitions from sample
Possible value | Meaning |
---|---|
0 | Use all reads |
1 | Remove transitions |
Set a seed value for creating approximate inbreeding coefficients
Any positive integer or $RANDOM
Perform sliding window Thetas calculations
Possible value | Meaning |
---|---|
true |
Use a sliding window |
false |
Do not use a sliding window |
Set the maximum p-value for polymorphic sites
Any positive floating point value
Set the step size for sliding window analysis
Any positive integer
Use only uniquely-mapped reads
Possible value | Meaning |
---|---|
0 | Do not restrict to uniquely-mapped reads |
1 | Restrict analysis to uniquely-mapped reads |
Set the sliding window size
Any positive integer