Description

Estimate site allele frequencies from BAM files.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

0 ()

1 ()

0 ()

1 ()

error_file (file)

A file containing per-base substitution error rates for use with the Sykes genotype likelihood model (-GL 4).

*.errors

inbreeding_coefficients (file)

A file containing estimates of individual inbreeding coefficients.

*.indF

soapsnp_calibration (directory)

Directory of soapSNP calibration files. Required for use with the SOAPsnp genotype likelihood model (-GL 3), passed to ANGSD via -tmpdir. Contains (per sample), a .counts file of per-position base/allele counts and a .qual file of recalibrated quality score information.

*_calibration_matrix

gl_model (integer)

Genotype likelihood model to use (angsd -GL). 1=SAMtools, 2=GATK, 3=SOAPsnp, 4=SYK.

dosaf_mode (integer)

Site allele frequency likelihood estimation mode (angsd -doSAF). 1=standard, 2=inbreeding-aware (requires indF).

Output

Name
Description
Pattern

0 ()

0 ()

Tools

angsd Documentation

ANGSD: Analysis of next generation Sequencing Data

https://github.com/ANGSD/angsddoi: 10.1186/s12859-014-0356-4License: GPL v3, MIT
Authors