BayesAss for RADseq Data

I want to use BayesAss on a large SNP dataset generated with RADseq.  But I found out when I went to convert the data into the .immaq format that my favorite converter, PGDspider, would only convert the first 40 loci.  I didn’t get 10,000s of loci for nothing, so that wasn’t going to work.  But a second problem was that BayesAss 3.0.3 only allows 240 SNPs anyways.

Obviously I’m not the only person with this problem.  And thanks to Steve Mussmann there’s a solution.  Steve re-wrote BayesAss 3.0.4 to be able to handle large SNP datasets, as well as a program to convert the STRUCTURE files from pyRAD into .immaq input files for BayesAss.

Since I have STRUCTURE files from STACKS and not pyRAD, I had to do a little conversion.  My messy code is below, but leave a comment if you are a wiz with an elegant solution.

Turning STRUCTURE Output from STACKS into STRUCTURE Output from pyRAD
First, output data from STACKS in STRUCTURE format (.str).  Remove the first two rows from this output (STACKS header and loci identifiers).  Then, print the first column (sample names), insert five empty columns to match pyRAD.  Do not print the second column from the STACKS STRUCTURE output because that is the population code from your Population Map input into STACKS.

awk '{print $1 "\t" "\t" "\t" "\t" "\t" "\t"}' data.str > test.out

Next, print out the remainder of your data starting at column 3 (i.e. first locus) in the original dataset (awk code from here).  Then use paste to concatenate the two files into the .str file you will convert.

awk '{for(i=3;i<NF;i++)printf"%s",$i OFS;if(NF)printf"%s",$NF;printf ORS}' data.str | tr ' ' '\t' > test2.out

paste test.out test2.out > data.str

Convert .str to .immac Using a Custom PERL Script
If you already had data from pyRAD and did not have to do the steps above, you can just convert your .str file to an .immac using Steve’s script: str2immaq.pl. However, if you have data from STACKS then you need to modify lines 39-52 in the original script to the following:

# convert structure format to immanc format, and push data into hash
for(my $i = 0; $i < @strlines; $i++){
	my @ima;
	my @temp = split(/\s+/, $strlines[$i]);
	my $name = shift(@temp);
	foreach my $allele(@temp){
		push( @ima, $allele);
	}

Since STACKS exports missing data as 0 (whereas pyRAD exports missing data as -9), this change removes converting missing data from -9 to 0. Steve also wrote this change.  Save the change in the perl script, then use the script to convert data from .str to .immac.  Now you’ve got an input file for BayesAss.

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