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 we need seprate 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 that is it possible to do cohort analysis to run all unrelated samples together? Thanks in advance. Best, Ali

so I didn't make the pipeline but if I put multiple familys in the "sample sheet", it does default to the first one for all the file names, BUT the SV output file is a multi-sample VCF that includes variants across all samples provided

I checked it is the same case with the snv vcf the header suggests that it has varient calls for multiple samples, #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMS01 SAMS02 SAMS03, it seems like a combined varient call set of multiple samples.