Hello everyone, as anyone ever tried to resume a previous run appending only rna-seq data and knows what is the most efficient way of doing this is? Basically, I’ve run oncoanalyser with only wgs data (T-N), and now would like to run with new rnaseq data that I have but keeping some of the results I already have. I tested doing a samplesheet with the file types:

bam_redux

,

bai

,

redux_jitter_tsv

,

redux_ms_tsv

,

fastq

(for the new rna sample),

purple_dir

,

esvee_vcf

,

esvee_vcf_tbi

,

sage_vcf

,

sage_vcf_tbi

and

lilac_dir

. This worked but ran sage for the germline, didn’t run lilac and didn’t produce the Orange report. Then, I tried one more time, with a more exhaustive samplesheet where I basically just didn’t specify the

isofox_dir

,

lilac_dir

, and

cuppa_dir

. This worked much better but, again, didn’t produce the Orange report.

Hi Mafalda, thanks for your message! You should be almost there. The only thing missing is

sage_dir

(not the vcf files) and that should run ORANGE as well

Thank you Rayan, that solved it! I just have one more question. When I start an oncoanalyser run from these different starting points, some of the tools have multiple options of directories. For example, to reuse the BAMTOOLS result, I can specify

bamtools_dir

but this has to be the directory for the tumor sample, so BAMTOOLS ends up running for the normal sample. Similar things happen for SAGE, for example. Is there anyway to prevent this from happening to have a more efficient run? Or does it have a reason that I am overlooking?

Hi Mafalda, yes - depending on your samplesheet contents, the pipeline infers whether the

bamtools_dir

belongs to your tumor or your normal. You'd need to provide a different filetype for both. Thi happens for a number of tasks for which a process runs for both the tumor and the normal. An example samplesheet to avoid it for BAMTOOLS or SAGE would be as follows:

group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
  PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bamtools_dir,/path/PATIENT1-T.bamtools/
  PATIENT1,PATIENT1,PATIENT1-N,normal,dna,bamtools_dir,/path/PATIENT1-N.bamtools/
  PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,sage_dir,/path/PATIENT1-T.sage/
  PATIENT1,PATIENT1,PATIENT1-N,normal,dna,sage_dir,/path/PATIENT1-N.sage/
  PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,linx_anno_dir,/path/PATIENT1-T.linx/
  PATIENT1,PATIENT1,PATIENT1-N,normal,dna,linx_anno_dir,/path/PATIENT1-N.linx_germline/

Can you try it and let me know if it helps ?

Hi Rayan, thank you. I've tried with bamtools for normal and it worked. Thank you for your help!