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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Missing ID for evidence of PE reads. #254

Closed zhliUU closed 6 years ago

zhliUU commented 6 years ago

Hi,

When printing the evidences for inversion with -e, I could see the IDs for split reads but not for paired-end reads. Is there any way to get the IDs of PE? wechatimg55

ryanlayer commented 6 years ago

You can use SVTYPER to get that info.

On Jul 10, 2018, at 9:32 PM, zhiwei notifications@github.com wrote:

Hi,

When printing the evidences for inversion with -e, I could see the IDs for split reads but not for paired-end reads. Is there any way to get the IDs of PE?

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zhliUU commented 6 years ago

Maybe I wasn't clear about IDs I need.

I was looking for the reads name for the paired-end reads as shown in the second column for SR in the figured I uploaded. From SVTYPER I only got a bunch of statistic e.g GT:SU:PE:SR:GQ:SQ:GL:DP.... I will have to look into IGV if there is no convenient way to print them.

Thanks.

ryanlayer commented 6 years ago

Right. Sorry. You can pass an option to SVTYPER and it will create a bam of just the reads you want.

On Jul 11, 2018, at 12:58 AM, zhiwei notifications@github.com wrote:

Maybe I wasn't clear about IDs I need.

I was looking for the reads name for the paired-end reads as shown in the second column for SR in the figured I uploaded. From SVTYPER I only got a bunch of statistic e.g GT:SU:PE:SR:GQ:SQ:GL:DP.... I will have to look into IGV if there is no convenient way to print them.

Thanks.

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