Hi all. Quick question. Is

rnavar

suitable for variant calling in FPPE-derived samples? I read a bit about FPPE-derived samples, and they have their challenges. Thanks in advance.

FFPE samples generally suck, but if that's what you have, you have to deal with it. If you are interested in germline variants, that is easier (you don't have to distinguish low-frequency variants from artifacts), and the pipeline should serve you well (maybe do some filtering on the results), although bad coverage is still an issue. Since at this point the only SNP/indel caller is the GATK HaplotypeCaller, this is not ideal for somatic variants.