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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Use single-end reads aligned with bwa-aln #355

Open jcchacond opened 3 years ago

jcchacond commented 3 years ago

Hello,

Is it possible to use LUMPY-SV on single-end reads aligned with bwa-aln? Is it possible to use it only with read-depth information?

I read in a reply to an issue (110; resolved) that LUMPY-SV can be used in single-end data "as long as it has been aligned with a split-read aligner" (like bwa-mem). I work with ancient DNA data where sequencing reads tend to be shorter than 70bp (hence the use of bwa-aln) and are routinely merged before alignment and treated as single-end reads.

Thanks in advance for your help, Camilo

ryanlayer commented 3 years ago

Can you reach out to me personally so we can discuss? Ryan dot layer at Colorado

On Feb 19, 2021, at 5:20 AM, Camilo Chacon-Duque notifications@github.com wrote:

 Hello,

Is it possible to use LUMPY-SV on single-end reads aligned with bwa-aln? Is it possible to use it only with read-depth information?

I read in a reply to an issue (110; resolved) that LUMPY-SV can be used in single-end data "as long as it has been aligned with a split-read aligner" (like bwa-mem). I work with ancient DNA data where sequencing reads tend to be shorter than 70bp (hence the use of bwa-aln) and are routinely merged before alignment and treated as single-end reads.

Thanks in advance for your help, Camilo

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