Input

ANSGD currently supports various mapped data, genotype likelihood formats and imputed genotype probability files

Mapped sequence file

bam files

ANGSD accepts bam files for mapped sequences. For imformation on the file specification and file creation see the samtools website [1]

arguments

To include a beagle file us the option

-bam [filelist]

The filelist is a file containing the full path for each bam file with one filename per row.

Example of a filelist with 6 individuals

/home/software/angsd/test/smallBam/smallNA12763.bam
/home/software/angsd/test/smallBam/smallNA11830.bam
/home/software/angsd/test/smallBam/smallNA12004.bam
/home/software/angsd/test/smallBam/smallNA06985.bam
/home/software/angsd/test/smallBam/smallNA11993.bam
/home/software/angsd/test/smallBam/smallNA12761.bam

Example of estimating allele frequencies from bam files

./angsd -outfiles out -doMaf 2 -bam bam.filelist

obtional arguments

-r [region]

Specify a region with in a chromosome using the syntax [chr]:[start-stop]

-only_proper_pairs [int]=0

-rf [region file]

specify multiple regions in a file.

-nLines [int]=50

Number of lines to read per file at a time. Reducing this number will decrease the RAM usage with a small cost to the speed.

-uniqueOnly [int]=0

remove reads that have multiple best hits.. 0 no (default), 1 remove

-remove_bads [int]=1

Same as the samtools flags -x which removes read with a flag above 255 (not primary, failure and duplicate reads)

genotype probability files

beagle format

Genotype probabilities in beagle format can be used as input. The format used is the haplotype imputation format outputted from beagle [2].

options

To include a beagle file us the option

-beagle [file]

example

The file format is a single linje per site. The first 3 coloums are

• markerName
• alleleA
• alleleB

For each individual 3 coloums are added. These three colums should sum to one.

Example of a file with two individuals

marker alleleA alleleB NA06984 NA06984 NA06984 NA06986 NA06986 NA06986
chr9_95759065 G A 0.6563 0.3078 0.0358 0.5357 0.4016 0.0627
chr9_95759152 C A 1 0 0 0 1 0
chr9_95762332 G A 0.925 0.0734 0.0015 0.894 0.1031 0.0029
chr9_95762333 A T 0.8903 0.1067 0.003 0.811 0.1797 0.0093
chr9_95762343 G T 0.9149 0.0835 0.0017 0.8396 0.1541 0.0064

Example of estimating allele frequencies from beagle files

./angsd -outfiles out -doMaf 16 -beagle file.beagle