I discovered a de novo deletion from my trio BAM files (long reads) using samplot. This deletion was not detected by the long read SV caller I used. I only used a samplot plot program for a region which that had a prospective deletion from short read sequencing. From the paper, I read that:
"Samplot includes a background track with up to base-pair resolution of the fluctuations in coverage depth across the plot region. Samplot follows a minimal decision-making strategy and makes no computational attempt to assign reads or coverage deviations to putative variant coordinates; this task is left instead to the user via visual curation."
I was hoping if this could be elaborated in any way on how did Samplot discover the SV from the BAM file. Can I interpret that samplot used the split reads and coverage depth of my long read sequencing into account to indicate that there is a potential deletion in that region? Just wondering if samplot can be used as an orthogonal approach to confirm the presence of an SV if an SV was found using some different technology and analysis pipeline.
Hi,
I discovered a de novo deletion from my trio BAM files (long reads) using samplot. This deletion was not detected by the long read SV caller I used. I only used a samplot plot program for a region which that had a prospective deletion from short read sequencing. From the paper, I read that:
"Samplot includes a background track with up to base-pair resolution of the fluctuations in coverage depth across the plot region. Samplot follows a minimal decision-making strategy and makes no computational attempt to assign reads or coverage deviations to putative variant coordinates; this task is left instead to the user via visual curation."
I was hoping if this could be elaborated in any way on how did Samplot discover the SV from the BAM file. Can I interpret that samplot used the split reads and coverage depth of my long read sequencing into account to indicate that there is a potential deletion in that region? Just wondering if samplot can be used as an orthogonal approach to confirm the presence of an SV if an SV was found using some different technology and analysis pipeline.
Regards, Prasun