How to further process data after the variant calling on .bams?

Question

[vassialk]

How to further process data after the variant calling on .bams? We have tuberculosis WGS data. What are the proper tools for the visualization and further analysis of variant calls?

[Evgeniia Golovina]

You can annotate tuberculosis variant VCF files using SnpEff.

There are a plenty of tools for data visualization. You can review some of them here.

[mkulecka]

First of all, you may want to filter out false positive variant calls. You can use this tool: https://github.com/ckandoth/variant-filter or other variant filters (from GATK for example).

Visualization: IGV or GoldenHelix Genome Browse.

Answer 1

[TriS]

First I would ask you how did you (or someone else) call the variants? Which file format(s) do you have? Is that VCF or tool-specific output? Do you have normal and diseased samples? Which questions are you asking? Are you looking for GUI or command line tools?

For a comprehensive output, that returns a MAF format that you can use in IGV (link in comment above), you can use oncotator from Broad. for a command line tool you can use annovar and, as mentioned above, SnpEff.

Or the Variant Effect Predictor at Ensembl which is GUI and contains both SIFT and PolyPhen