Very high read count variation in WGS alignments
I am new to NGS analysis, but have tried to learn through test data before starting with my own data. And now, it seems I am stuck somewhere. So, looking for some help/suggestions/ideas for the same.
I have few patient samples (Human) for which WGS was performed and I am trying to understand the underlying variations in the same. The data that I had received from the sequencing company was performed in multiple libraries (2) and multiple lanes (2-6). I individually performed QC for all fastq files and then started aligning them separately using bwa mem w.r.t. hg38 reference genome (chrX). After individually aligning them, I merged and sorted them using samtools for further variant calling.
But now, when I visualize the alignment files I notice a great variation in the read count for all the samples.
I have no idea why it is happening this way. Is there something that is wrong with the protocol I am following or can it be because of some issue in library prepartion?
Has anybody else experienced this or have any suggestions which might suggest what I am doing wrong here?
Any leads/inputs would be greatly appreciated.
Thanks in advance,
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