Running Multiple Singleton Samples with once CSV file

[bioinformaticsguy]

Greetings,

I was trying to run multiple unrelated singleton samples in one CSV file. The pipeline works fine initially, it does the alignment for each sample separately and also generates the multiqc report but the SNV_calls as well as the SV calls are only done for the first sample (S001). I just wanted to confirm if it is possible to run multiple samples using one CSV or if we need separate CSV files for each sample.

sample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id
S001,1,/data/S001.R1.fq.gz,/data/S001.R2.fq.gz,0,2,0,0,case_S001
S002,1,/data/S002.R1.fq.gz,/data/S002.R2.fq.gz,0,2,0,0,case_S002
S003,1,/data/S003.R1.fq.gz,/data/S003.R2.fq.gz,0,2,0,0,case_S003

Secondly, I wanted to ask if it is possible to do a cohort analysis and run all unrelated samples together.

I really appreciate any help you can provide.

Best,
Ali

[ramprasadn]

Hi Ali! Currently, raredisease does not support running multiple cases in a single CSV file. You will have to create a separate CSV file for each case.

Raredisease does not support cohort analysis either. Are you simply interested in calling variants from unrelated samples and doing a joint calling? In that case, you might be able to treat them all as if they are from the same case. And that should work I think.