I have several tumor samples sequenced alongside matched normal tissue.
This is starting with 100bp paired end Illumina .fastq files.
What would be a relatively straightforward way to visualize mutations that are tumor specific? I realize there are workflows for this and it may require several steps, but I am curious to hear others' opinions and I am open to ideas or software suggestions.
I would like to set the threshold relatively high, meaning I would only like to report results if the sample/gene/region is really mutated.
Of course there are many genetic aberrations in tumors including point mutations, insertions/deletions, copy number changes, and rearrangements.
Hopefully there is a relatively simple method to detect at least some of these using matched normal samples as a filter or control for the tumor samples. Meaning, reported results are mutations that are present in the tumor sample compared with the normal sample, rather than mutations compared with the reference genome, for example.
All advice is appreciated, thank you.
This is starting with 100bp paired end Illumina .fastq files.
What would be a relatively straightforward way to visualize mutations that are tumor specific? I realize there are workflows for this and it may require several steps, but I am curious to hear others' opinions and I am open to ideas or software suggestions.
I would like to set the threshold relatively high, meaning I would only like to report results if the sample/gene/region is really mutated.
Of course there are many genetic aberrations in tumors including point mutations, insertions/deletions, copy number changes, and rearrangements.
Hopefully there is a relatively simple method to detect at least some of these using matched normal samples as a filter or control for the tumor samples. Meaning, reported results are mutations that are present in the tumor sample compared with the normal sample, rather than mutations compared with the reference genome, for example.
All advice is appreciated, thank you.