bedgraph and bedmethyl only-tab simultaneously

[ShokodkoMariia]

Hello, is there any possibility to get both .bedgraph and .bedmethyl (only-tab) from one run of the tool (while doing one command)? If there isn't any, could you add it later?

[ArtRand]

Hello @ShokodkoMariia,

This is a pretty common request, so I'll try and get it into an upcoming release.

In the mean time, you can convert the bedMethyl file into a bedGraph since the bedGraph contains a subset of the information.

awk -v OFS="\t" '{print $1, $2, $3, $11, $10}' $bedmethyl

[marcus1487]

You can use modkit pileup ${bam_path} - | tee out.bedmethyl | awk -v OFS="\t" '{print $1, $2, $3, $11, $10}' > out.bg to get both outputs at once without running anything twice.