Question: Assigning a "sample_name" column dynamically in the SAM tool generate pileup
2
gravatar for gkuffel22
2.7 years ago by
gkuffel22170
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 • 695 views
ADD COMMENTlink modified 2.7 years ago by Jennifer Hillman Jackson23k • written 2.7 years ago by gkuffel22170
1
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

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 2.7 years ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 116 users visited in the last hour