Variants in untargeted genes identified after atrgeted exome sequencing analysis

Hi,

I recently analyzed some targeted exome sequencing samples, which were provided to us by our collaborators, for which I do not possess the target gene list. Upon analysis, I am informed that some of the genes - whose variants were identified - were not present in the target gene list. Has anyone ever faced such an issue, or have any idea why I might be observing these variants?

If it helps, I had found duplicate entries (both name and sequence) in some raw fastq files, so I had removed them using seqkit rmdup. Since I don’t know whether all variants in untargeted genes exist exclusively in these files, I can’t even be sure that removing the duplicate entries could be causing an issue with the alignment and/or variant calling.

The pipeline used was – fastqc –> trim_galore (while preserving only the paired reads, and not singular reads) –> seqkit rmdup -n (to remove duplicate entries based on name) –> bwa_mem using hg38 as the reference –> picard to sort_sam, mark and remove PCR duplicates –> variant calling with GATK4 –> BQSR with GATK4 –> applying BQSR on bam file with GATK4 –> variant calling from the recalibrated bam file created in the previous step using GATK4 –> annotation using hg38 as a reference with wANNOVAR

Thanks in advance.