How to set soft-clipped bases option in IGV batch script

Question

[JellyFrog]

Hi,

I would like to view soft clipped bases in BAMs. I know I can click View-Preference-Alignments-Show soft clipped bases for an individual BAM, but I would like to enable it and take snapshots for a list of BAMs. Is there an option in the batch script to achieve it?

Thanks in advance,

J

Answer 1

[Pierre Lindenbaum]

(not tested) can you please try:

preference SAM.SHOW_SOFT_CLIPPED true

[JellyFrog]

Works like a charm. Thank you.

[Pierre Lindenbaum]

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