bedtools genomecov per-base report in igv

Question

[pyKey]

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,

Answer 1

[ATpoint]

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.