angsd

This is the primary program for analyzing the data from a population genetics standpoint. Be wary of what version you have (on the server or in your local) as scripts may/may not work with different versions, you may need to update.

There are many angsd calls and modules that we can use, there are flags/arguments for different things and different analyses. Just as a quick overview of what a call to angsd might look like here’s an example PCA call:

• angsd -out outFileName -bam bam.filelist -GL 1 -doMaf 1 -doMajorMinor 1 -minQ 20 -minMapQ 10 -doMaf 2 -doPost 2 -doGeno 32 -minMaf 0.05 -postCutoff 0.95 -SNP_pval 1e-6

Bear in mind the numbers are often additive, so you can sum the various options together to get an output you want. For example, -doGeno 5 is (1+4), and prints the major and minor allele followed by the genotype (AA, AC …) for each individual.

See the angsd wiki for more info.

Analyses with angsd

Generally we mainly use angsd for:

• SNP/Genotype calling
• Generating PCA data
• SFS Estimation
• Calculating Thetas/Tajimas
• Calculating FST
samtools & bedtools
We use samtools for many different things, but primarily for reading/editing/viewing SAM/BAM read files.
We use bedtools for merging our different sequencing runs. There’s a bunch of great documentation for these tools here.