FAQ

Question: Will angsd-wrapper be updated on a regular basis?

Answer: Yes! A second version is already in the works; this version will include simplified configuration files and work with the latest version of ANGSD.

Question: Can I use my own version of ANGSD?

Answer: No, you should use the version of ANGSD included with angsd-wrapper.

Question: When I try to compile ANGSD, the following error is reported: /usr/bin/ld cannot find -lz

Answer: Generally this error appears when your system doesn't have the required version of zlib. If you are working on computing cluster, contact your system administrator.

Question: How do I call SNPs using ANGSD and angsd-wrapper?

Answer: ANGSD was designed to perform most population genetic analyses without the need to make SNP calls. That is, variants are dealt with probabilistically and many common descriptors of polymorphism in a population can be calculated without SNP calls. SNP calling is possible in ANGSD and with the help of angsd-wrapper. See the tutorial for details.

Question: Where can I find the step-by-step process for running angsd-wrapper?

Answer: We are working on tutorials that will demonstrate the most common analyses conducted with ANGSD and angsd-wrapper.

Question: Do I need an outgroup sequence to use ANGSD and angsd-wrapper?

Answer: It is necessary to have an outgroup sequence to infer the ancestral state of the mutations and to estimate the derived site frequency spectrum. However, many of the descriptive statistics calculated by ANGSD are not dependent on the ancestral state of mutations. If not outgroup sequence is available, include the path to the reference sequence when asked for the outgroup.

Question: Do I need to include inbreeding coefficients in my analyses?

Answer: Yes, angsd-wrapper requires the input of inbreeding coefficients in most analyses. If you prefer not to incorporate inbreeding, create a file with 0 on a new line for each individual in your population(s), i.e. assume complete outcrossing, and link to this file in the required places.

Question: ANGSD complained about not being able to find a chromosome even though it's in my reference sequence.

Answer: This issue is caused by out of order chromosomes in your reference. You can fix this in the following way:

for i in `seq 1 12`; do samtools faidx ref.fa $i >> sorted_ref.fa; done

Where 12 is the number of chromosomes. Then gzip your fasta and run

samtools faidx sorted_ref.fa.gz

to get your .fai file.