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Calling whole-genome haplotypes for Chloroplast-captured Pooled Samples
I'm trying to call whole-chloroplast genome haplotypes for a pooled chloroplast-captured DNA sample from a non-model organism (no well-established variants). The reads are Illumina 100 bp PE reads, and have already undergone some clipping (adapter-trimming and quality control) and have been aligned to a reference genome. The pool represents 20 individuals. I want to know if there is a way in GATK to call the frequency of whole-genome haplotypes (or else, is there a way currently in existence elsewhere? ) If necessary, I can generate a panel of known haplotypes.
Currently, I have been using HaplotypeCaller to call SNPs and then filtering those by hand in Excel. I have already tried increasing the maximum active region size to larger than the whole reference genome (~150,000 bp), with a corresponding increase in the max reads per sample value, but this doesn't seem to have come up with whole-genome haplotypes.