This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to visualize bam, bed and vcf files programmatically using Python and Shell or a Linux software?

How to visualize bam, bed, and vcf files programmatically using Python and Shell or a Linux software? Have these files coming from the NGS microbial data processing pipeline, need to make charts and plots from them, looking for a proper robust software packages for Linux OS.

software visualization bam vcf bed
• 1,843 views • link
updated by dariober dariober • written by informatics_warwick • informatics_warwick

What you mean by "visualize programmatically"?, however, to visualize bam or bed files you can use IGV, you can visualize more than one file at the same time (if you mean that).

• 0 views • link
written by Buffo Buffo

For anyone using Windows, EaSeq has some nice functionality to do this with different sorts of visualizations outside of just tracks. Unfortunately, it's a Windows only program.

• 0 views • link
written by jared.andrews07 jared.andrews07

Hello informatics_warwick!

We believe that this post does not fit the main topic of this site.

Not a real question

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by Michael Dondrup Michael Dondrup

2 answers

RSeQCoffers a variety of graphics for alignment QC. Some of the tabular output files can afterwards be nicely visualised using multiQC.

• 0 views • link
written by michael.ante michael.ante

Assuming that by "visualize" you mean showing coverage and/or alignments in genomic windows, you can use Gviz if you are ok with R. For quick, explorative visualization directly from the command line I wrote ASCIIGenome.

• 0 views • link
written by dariober dariober

Log in to answer this question.

More posts like this