When I viewed a BAM file with samtools view to examine reads aligned to the reference genome within a CNV region,
I noticed that some reads appeared with underlines, which, upon checking their SAM flags, indicated they were "not primary alignment (0x100)."
The plain white characters represent the nucleotide sequence, but I'm unsure about the meaning of the blue, underlined reads.
Could you advise if viewing the wf-human-variation result file with samtools view is not recommended, or explain what those blue underlined characters signify?
I apologize for my ignorance and thank you for always responding kindly.
cjw85
commented
1 month ago
Ask away!
When I viewed a BAM file with
samtools viewto examine reads aligned to the reference genome within a CNV region, I noticed that some reads appeared with underlines, which, upon checking their SAM flags, indicated they were "not primary alignment (0x100)." The plain white characters represent the nucleotide sequence, but I'm unsure about the meaning of the blue, underlined reads. Could you advise if viewing the wf-human-variation result file withsamtools viewis not recommended, or explain what those blue underlined characters signify?I apologize for my ignorance and thank you for always responding kindly.