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Parameters

mojaveazure edited this page Jun 1, 2016 · 7 revisions

This is a list of all possible parameters for various methods in ANGSD-wrapper

BAQ

Function

Calculate base alignment quality

Legal Values

Possible value Meaning
0 Do not calculate BAQ score
1 Standard BAQ score
2 Extended BAQ score

Methods that use this parameter

BLOCKSIZE

Function

Set the size for each block

Legal Values

Any integer higher than the linkage disequilibrium

Methods that use this parameter

CALL

Function

Perform genotype calling

Legal Values

Possible value Meaning
0 Do not call genotypes
1 Call genotypes

Methods that use this parameter

DO_ABBABABA

Function

Perform Abbababa analysis

Legal Values

Possible value Meaning
1 Perform Abbababa

Methods that use this parameter

DO_COUNTS

Function

Count allele frequencies

Legal Values

Possible value Meaning
0 Do not count allele frequencies
1 Count allele frequencies

Methods that use this parameter

DO_FASTA

Function

Extract FASTA sequence from BAM file

Legal Values

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

Methods that use this parameter

DO_GENO

Function

Call genotypes from genotype likelihoods

Legal Values

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

Methods that use this parameter

DO_GLF

Function

Output genotype likelihood frequency file

Legal Values

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

Methods that use this parameter

DO_MAF

Function

Calculate allele frequencies

Legal Values

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

Methods that use this parameter

DO_MAJORMINOR

Function

Determine major and minor alleles

Legal Values

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

Methods that use this parameter

DO_POST

Function

Calculate the posterior probability

Legal Values

Possible value Meaning
0 Calculate posterior probability from genotype probabilities
1 Use the per-site frequency as a prior
2 Use a uniform prior

Methods that use this parameter

DO_SAF

Function

Generate site allele frequencies

Legal Values

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

Methods that use this parameter

GT_LIKELIHOOD

Function

Calculate genotype likelihoods

Legal Values

Possible value Meaning
1 Use SAMTools model for genotype likelihoods
2 Use GATK model
3 Use SOAPsnp model
4 Use SYK model

Methods that use this parameter

GLOBAL

Function

Calculate global Fst values

Legal Values

Possible value Meaning
true Calculate global Fst values
false Do not calculate global Fst values

Methods that use this parameter

K

Function

Set the number of assumed populations to estimate Admixture under

Legal Values

Any integer greater than or equal to 2

Methods that use this parameter

MIN_BASEQUAL

Function

Set the minimum base quality

Legal Values

Any positive integer

Methods that use this parameter

MIN_EPSILON

Function

Set the minimum root-mean-square deviation between to assume convergence

Legal Values

Any positive floating point value

Methods that use this parameter

MIN_IND

Function

Set the minimum number of individuals required

Legal Values

Any positive integer

Methods that use this parameter

Note: Fst Estimations have two MIN_IND fields, one for each population

MIN_MAF

Function

Set the minimum minor allele frequency

Legal Values

Any positive floating point value

Methods that use this parameter

MIN_MAPQ

Function

Set the minimum mapping quality for a base to be used

Legal Values

Any positive integer

Methods that use this parameter

N_CORES

Function

Set the number of threads and cores to be used by ANGSD-wrapper

Legal Values

Any positive integer less than or equal to the number of CPU cores on your system

Methods that use this parameter

N_SITES

Function

Set the maximum number of sites to use for Principal Component Analysis

Values

Any positive integer

Methods that use this parameter

NORM

Function

Normalize by allele frequency

Legal Values

Possible value Meaning
0 Do not normalize by allele frequency
1 Normalize by allele frequency

Methods that use this parameter

OVERRIDE

Function

Overwrite any previously generated results

Legal Values

Possible value Meaning
true Overwrite previous results
false Do not overwrite previous results

Methods that use this parameter

POST_CUTOFF

Function

Set the minimum posterior value for calling genotypes

Legal Values

Any positive floating point value

Methods that use this parameter

REMOVE_TRANS

Function

Remove transitions from sample

Legal Values

Possible value Meaning
0 Use all reads
1 Remove transitions

Methods that use this parameter

SEED

Function

Set a seed value for creating approximate inbreeding coefficients

Legal Values

Any positive integer or $RANDOM

Methods that use this parameter

SLIDING_WINDOW

Function

Perform sliding window Thetas calculations

Legal Values

Possible value Meaning
true Use a sliding window
false Do not use a sliding window

Methods that use this parameter

SNP_PVAL

Function

Set the maximum p-value for polymorphic sites

Legal Values

Any positive floating point value

Methods that use this parameter

STEP

Function

Set the step size for sliding window analysis

Legal Values

Any positive integer

Methods that use this parameter

UNIQUE_ONLY

Function

Use only uniquely-mapped reads

Legal Values

Possible value Meaning
0 Do not restrict to uniquely-mapped reads
1 Restrict analysis to uniquely-mapped reads

Methods that use this parameter

WIN

Function

Set the sliding window size

Legal Values

Any positive integer

Methods that use this parameter

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