How to call heterozygous SNPs
We sequenced and assembled a genome. Now, I'm interested to call all heterozygous SNPs of the same genome. For that, I mapped paired end reads (same reads used for the genome assembly) back to the same genome. Is there a pipeline to call these heterozygous SNPs?
I appreciate any sort of help.
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If you are re-mapping the same reads, wouldn't any SNP you find technically be a het SNP? For example, if your assembly has a consensus base G at a locus but when you re-map the reads you find a G/A SNP at the same site, then this is a heterozygous site. Right? If no, please explain what your expected pipeline and results are.
That, or an error due to misassembly.
Variant calling best practices for WGS & WES
If you are expecting notable heterozygosity in your genome, I wonder how you dealt with it in the assembly process. There are heterozygosity aware assembly pipelines that could incorporate heterozygous variant discovery in the assembly process.