Question: Assigning a "sample_name" column dynamically in the SAM tool generate pileup
gravatar for gkuffel22
3.7 years ago by
United States
gkuffel22170 wrote:

Hi everyone,

I am creating a workflow in Galaxy that I will be using for variant analysis for about 200 samples. I have just hit another road block and I'm hoping someone can help. After I run  BWA, I use the output (a BAM file) to generate a pileup. From here I would like to filter and concatenate the datasets. My problem is, the pileup does not include a column for sample name. I tried to use the tool "Add column" under Text Manipulation but this can only be assigned manually. I attempted to use the variable #{input name} in this field in hopes that this could dynamically add the correct sample name to the column as samples were processed in the workflow. Instead, the tool doesn't behave as I hoped and does not recognize this variable and this added column reads "input" for every sample processed. Any advice or suggestions would be appreciated.

galaxy samtools • 951 views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by gkuffel22170
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


If you generate a bcf dataset instead with Mpileup (option: Compute genotype likelihood computation), the sample names in the inputs will be propagated to the results. Convert bcf -> vcf with the tool "SAMtools -> bcftools view". Other manipulations with vcf datasets can be done with tools under the group "NGS: VCF Manipulation".

There are two workflow variables for renaming a dataset (note: this renames a dataset, it does not change the content of a dataset). Still, these are useful for tracking outputs and if you want to try them, this prior post has the details for correct usage: 
Carrying a sample name through a workflow

Best, Jen, Galaxy team


ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
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