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

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,

igv

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updated 3.6 years ago by Pierre Lindenbaum

• written 3.6 years ago by JellyFrog •

1 answer

(not tested) can you please try:

preference SAM.SHOW_SOFT_CLIPPED true

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written 3.6 years ago by Pierre Lindenbaum

Works like a charm. Thank you.

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written 3.6 years ago by JellyFrog •

"Please accept the answer so the question is marked solved on the website. To do that, click on the green check mark on the left side of the answer."

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written 3.6 years ago by Pierre Lindenbaum

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