Dear Melanie
Thank you for this amazing pipeline.
I have some questions regarding how to run the pipeline (I am new to using Snakemake).
For the pipeline, do you recommend including all samples in the data.yaml file?
How can I run from a specific step? (Considering that I have the sorted bam files of the first step)
If I run the pipeline for each sample independently, does the step "mark_specific_in_raw" need the list of other vcf files?
When I tested the pipeline with two samples, the final output was not the merged vcf. Is there any flag I need to use to run this step, or should I run it independently?
Finally, If I run all the steps independently, should I merge all ism vcf files and all ism.specific vcf files into a unique vcf?
Dear Melanie Thank you for this amazing pipeline. I have some questions regarding how to run the pipeline (I am new to using Snakemake).
For the pipeline, do you recommend including all samples in the data.yaml file? How can I run from a specific step? (Considering that I have the sorted bam files of the first step) If I run the pipeline for each sample independently, does the step "mark_specific_in_raw" need the list of other vcf files?
When I tested the pipeline with two samples, the final output was not the merged vcf. Is there any flag I need to use to run this step, or should I run it independently?
Finally, If I run all the steps independently, should I merge all ism vcf files and all ism.specific vcf files into a unique vcf?
Thank you in advance!