Haplotype analysis

[jennaj]

Hi @cgreig

Let’s go through these, and if you solved some already, please let us know!

@cgreig

I have been checking the resultant ts/tv ratio as a quality metric - what would you recommend to compare quality of vcf files?

These tools seem like good choices:

1. VCFcommonSamples: Output records belonging to samples common between two datasets
2. You could also run one of the VCF report tools, maybe on just a sliced region, and inspect that in a genome browser like IGV. Known regions could be interesting such as a particular gene, or class of genes.

@cgreig

I’ve had a couple of further galaxy issues:- one I hope you might be able to help me with. I have been using BCF tools stats and was hoping to compile results using MultiQC, but whatever I try, I am getting average results for my files rather than a comparison. Is it possible to do this?

The “sample merging/ignoring” issue happens with MultiQC anywhere, not just in Galaxy, and comes up occasionally here at this forum. Recent example from last week involving a custom report MultiQC not displaying all elements in a table - #2 by jennaj and another that used a different kind of standard report multQC issue and guidance?

MultiQC expects distinct sample identifiers per report. Changing the file name before running the upstream statistics tool is usually enough. If the data is in a collection, that would mean adjusting the element identifiers. I can share instructions for this – so let me know if you need help with it. Seeing the data in history might help.

@cgreig

I have set up an EU account and been able to transfer one of my samples and run Snippy on it but had trouble with exporting a history (even a very small one) for several days. I also had trouble with some tools that failed sporadically (principally VCF-VCF intersect). I’m not sure there is still a problem, but I thought I’d better report it. I have just managed to export a history so that is good news!

There were some issues at the ORG server last week that are now resolved. I would try all of that again as a first pass solution, and we can troubleshoot more about anything persistent. Server issue UseGalaxy.org March 17 2025: RESOLVED

@cgreig

however the exact information is not clearly given in many papers,

Yes, this is unfortunately the “state of reproducibility” for computational biology experiments. Wet lab work will have exact details, but the bioinformatics, not so much!

The best resource is the tool manual itself, and direct experimentation, plus publications (where the latter is only as good as the previously published work is, as you noticed). You could also search scientific forums for advice. This forum is mostly about getting things to work in Galaxy, not scientific advice, so the other experts working in your field will not see the discussions here.

Hope this helps anyway!