Hi all,
I have pooled RAD-seq data (multiple individuals sequenced in a single library prep) and I am interested in haplotype frequencies.
Reads have been mapped to a de novo reference and I have a BAM file for each population.
It seems reasonable to assume that haplotypes frequencies could be called from BAM files in a manner analogous to determining allele frequencies in sequenced pools; e.g. counts of different haplotypes in the sample.
However, I cannot seem to find any good software specifically designed to deal with pooled RAD data. GATK and HaploPool, for example, are extremely limited by ploidy size. Collen Beck's rad_haplotyper (https://github.com/chollenbeck/rad_haplotyper) is nice to use and good for RAD data but assumes individuals as the sequenced unit; at most it would only provide information about which populations are likely fixed for particular haplotypes.
Does anyone have good recommendations?
Cheers,
~ Josh
My two cents are that there is a scarce of software available for pooled data - No matter what reviews papers say. I'm working with Popoolation and Popoolation 2. Input is mpileup
Popoolation and Popoolation2 need a ref genome to run.
Getting individuals Haplotypes information with RAD Pool-seq data is not possible, I think.
You can try CRISP maybe, in order to extract pools allele frequencies.
Y.
@Ivan and @Yann: Thanks for comments. I am using Freebayes to call SNPs because it has an argument that considers the mapped BAM files as deriving from pooled samples. BUT I REALLY WANT HAPLOTYPES!
Also, I have worked with the Popoolation tools before, but my understanding is that they are better suited to projects where you have much larger contigs (e.g. choromosomes as opposed to RAD fragments).
It confuses me that so little has been done to achieve this gap in analysis tools.
- Badges
- Science method
- Similar topics
- Biological Science
- Ecology