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dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
BSD 3-Clause "New" or "Revised" License
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`BAM` file type #338

Closed bounlu closed 1 year ago

bounlu commented 1 year ago

Hi,

The doc says duplicate marked BAM file is needed as the input.

How about duplicate removed (deduplicated) BAM file? Will it work in the same with Delly?

tobiasrausch commented 1 year ago

Should be the same if both reads of a pair are removed.

bounlu commented 1 year ago

Thanks for the info.

Related to this, does base quality score recalibration affect the way delly works? How are the base quality scores used in delly? Do you suggest to input recalibrated BAM files?

tobiasrausch commented 1 year ago

Delly uses mapping qualities, base qualities are not used.