Question: Audit trail for Bioinformatics software tools
0
gravatar for kspata
10 days ago by
kspata40
kspata40 wrote:

Hi,

I analyze several samples every day for variant analysis using align to reference method. For this purpose I use different Bioinformatics software such as Bowtie2/BWA, Samtools, and Freebayes. Is there a way in which I can know which version of software was used to process a particular sample. This should work like an audit trail, informing say Sample1 was aligned using bowtie2 vX.X.X, Sample2 was analysed using Bowtie2 vX.X.Y, and so on.

For example

bowtie2 --version command gives the output of Bowtie2 installed on the system as follows:

/usr/local/bin/bowtie2-align-s version 2.2.2
64-bit

another approach,

samtools view -H sample.sorted.bam

@HD VN:1.0 SO:coordinate @SQ SN: reference LN: @PG ID:bowtie2 PN:bowtie2 VN:2.2.2 CL:"/usr/local/bin/bowtie2-align-s --wrapper basic-0 -x -I 0 -X 1000 --fr -p 16 --local --passthrough -1 /tmp/40466.inpipe1 -2 /tmp/40466.inpipe2"

Both these commands do not tell that Sample1 was processed using bowtie2, Sample2 was processed using Bowtie2 and so on.

I would like to get an audit trail, where I will know for each software which version was used to process which sample.

Thanks!!

ADD COMMENTlink written 10 days ago by kspata40
1

You could capture this information (bowtie2 --version) in your analysis master logs for projects. Unix command script can capture all interactive dialog from a terminal sessions. Standard error and standard output logs captured from the analysis should include this information and can be saved.

You could also use a workflow system like snakemake to capture/automate your interactions and log those actions.

ADD REPLYlink modified 10 days ago • written 10 days ago by genomax60k
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 2.3.0
Traffic: 1232 users visited in the last hour