I am having an issue with a sequencing run that when demultiplexed, aligned, and filtered each individual has 1-2 million reads, but these reads are predominantly on one chromosome. For background these are oncorhynchus mykiss and o. clarki samples. The 6th chromosome has an order of magnitude higher reads than the other chromosomes. The libraries were prepared for rad-seq (sbf1) with 19 plates on one novaseq 6000 lane.
The demultiplexing was done using deML. Aligning to the O. mykiss reference genome used bwa and filtering/sorting in samtools.
I can't figure out if the issue is a library prep issue, sequencing issue, or something that I am doing wrong in the splitting and creation of the bam files? If anyone has had a similar problem please let me know.