hi folks, I have 5 illumina sequencing fastq files. 1 is the parent and 4 are mutants. I alligned the sequence to the refenrence genome I have all the BAM bed etc etc files. I cleaned repetitive seq in the bam file with picard. what I would like to find are the variants (SNv and indels) that are present in each of the mutant strain but not in the parent. also I would like to have the variants just in the coding sequences. what program can I use?
-
-
You need just step 1 from this tutorial since you only want SNv. -
isnt this command comparing a bam file to the reference genome? what I want are the SNV/indels present in the mutant strain but not in the control strain.Comment
-
You are identifying changes w.r.t. a reference and then comparing those results to get the difference between your control and mutant results.Comment
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment