Hello GATK team,
This might be a very general and overrated question but I appreciate your input. I am working with natural populations of plants (expected highly heterozygous individuals) and an enriched genomic region which contains some promoters of interest together with transposons, duplications and a lot of expected indels and SVs, including a potential paralog for one of our BACs. Unfortunately the long read sequencing is not yet ready so I am using the 2*75pb data and our BAC sequences as references to test how close we can get with HaplotypeCaller to see some SNP and short indel calls for an association analysis. Our coverage distribution seems to be heavily biased towards areas with duplications and potential TE and most of the assemblers based on local assembly are thrown off by our data. I have use very strict mapping parameters to avoid this problem with missaligned reads, given that we can't discard the possibility of having hyper-variable regions.
I understand that aiming for genotype calls is dangerous given our kind of data and the lack of a genome reference, so I am aiming to include the genotype likelihoods into the association analysis. With HaplotypeCaller I get a vcf file for my population and an associated PL value. My question is basically if given our type of data, do you consider that the local assembly inherent to HaplotypeCaller will give us false positives variants in the final output? Do you have any suggestion or alternative tools to get genotype likelihoods (without local assembly?) and input those into an association analysis tool?
I really appreciate your insight.
Best,