How to deal with the multi-sample ? about qtlseqr

[bmansfeld]

Hi,
If I understand your question correctly, you have sequenced the parental lines (neither of which are the reference genome genotype) as well as the two F2 bulks.
You are now curious about filtering out SNPs in the parental lines that are not in the reference genome.

I recommend the following pipeline:

1. Align one or both parents to the reference genome
2. call Variants for that parent vs the Reference genome
3. Extract only the SNPs and exclude any INDELs (the indels will shift your sequence positions). Make sure to keep only the highest quality and confidence SNPs
4. use the FastaAlternateReferenceMaker tool from GATK or another similar tool to apply the SNPs on the the reference genome and define an alternate fasta file.
5. Align and call SNPs from your F2 bulks vs the new fasta you've just created.
6. proceed with the analysis as usual.

Hope this helps,
Ben

[yuanlizhanshi]

Got it ,Thank you very much.