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Large number of scaffolds for the reference genome for SNP calling pipeline
I am running the SNP calling pipeline from RNA-seq data. I used STAR for alignment. My reference genome is composed of 32012 scaffolds from which more than 30000 are contigs with length of less than 1000 bp. I first decided to delete these contigs and just keep the superscaffolds, scaffolds and contigs longer than 1000 bp but in the STAR manual, it was recommended to keep all the sequences because other types of RNA can be mapped to them, so, I have retained them.
I have run the rest of the pipeline using these 32012 scaffolds as my reference. However, for the last step which is variant calling, I am going to extract only scaffolds that map to chromosome Z, so, I will have sthg around 40 scaffolds.
As I don't know the algorithms behind GATK and picard, I was wondering whether using these large numbers of primary scaffolds may be problematic at some steps? I am sorry for this general question, I have run the pipeline and have not encountered any problem so far but I was wondering if there is anything specific that I should look into the outputs to make sure everything has gone very well.
Thank you in advance.