BAM file comparison
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4.4 years ago
Hadeel ▴ 10

Hello Biostarers. I am trying to compare BAM files for similarity. I am doing this to assess alignment from different pipelines. Is there a quick straightforward way to do this?

alignment BAM • 3.5k views
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What exactly are you trying to compare in them? Do you want to compare each alignment or just come up with a correlation score?

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I want to assess how similar the alignments are from files for the same sample but from different pipelines. An overall correlation score would be enough I guess.

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4.4 years ago
Botond Sipos ★ 1.7k

The wub package has a script for comparing BAM files. It does a coarse comparison of alignments (checks whether the start position of the alignments is close enough) and also calculates a "consistency score" (the fraction of bases which align the same way).

The package also has a simple long read simulator, which can give you the "true" alignments in SAM format.

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4.4 years ago
Hussain Ather ▴ 970

You could try using bamcoverage from deeptools to convert them to bigwig files and then visualizing them using IGV or UCSC Genome Browser.

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4.4 years ago

From BAM files, the simplest route would be multiBamSummary followed by plotCorrelation from deepTools. If you want a bit finer grained control, then you can use bamCoverage and the multiBigwigSummary before plotCorrelation instead. Full disclosure: I'm one of the deepTools authors.

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I'm looking to do something similar, but instead comparing bam-files of the same input reads mapped to different assemblies to see the fraction of reads mapping to all assemblies. I was thinking to pull out the names of all mapped reads from each bam-file and then maybe simply make a venn-diagram of the lists, but could I use deepTools for this perhaps?

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I've never implemented anything in deepTools that would be useful for this, sorry.

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