What metrics to use for comparing alignment-based methods and variant calling for WGS data

Question

[joe_genome]

Hello Community

I'm currently revising different alignment-based methods (e.g. BWA-Mem, Bowtie, Novoalign) and want to compare the outputs generated by these methods. I'm considering just using BCFtools for this but was wondering what I should be looking for specifically.

Furthermore, I'm interested in comparing variant calling methods, more specifically Samtools, GATK for indels and muTect2, and VarScan2 in the case of somatic variants, for this case I also wanted to know what I should be looking at specifically to compare methods. Are there any particular metrics I should use to analyze these comparisons, maybe with BCFtools?

Please note I am working with WGS data from cancer patients.

Thank you in advance.

[liorglic]

You could have a look at Qualimap - might give you some ideas.

Answer 1

[Istvan Albert]

I would recommend doing a literature search, there are a large number of publications on these topics:

• https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00791-w
• https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03704-1

and many others.

[joe_genome]

Thanks, Istvan, I'm going to dive into it a bit deeper with a literature review. Just wanted to know if anyone had any encounters with this before. Thanks again :)