How to further process data after the variant calling on .bams?
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6.7 years ago
vassialk ▴ 200

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?

software tuberculosis sequencing sequence • 1.9k views
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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.

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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.

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6.7 years ago
TriS ★ 4.6k

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

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