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bedtools genomecov per-base report in igv

Hi All,

Is there a way to transform the per-base report of an alignment file into igv-readable format? Original command:

bedtools genomecov -d -ibam sample_file > out_file

Thank you,

bedtools igv per-base report
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updated by ATpoint ATpoint • written by pyKey • pyKey

1 answer

Use option -bg to generate a bedGraph and then transform to bigwig using bedGraphToBigWig which can be read into IGV. Alternatively use bamCoverage from deeptools which essentially does the same but in one command.

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written by ATpoint ATpoint

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