Question: Remap Clipped Sequence
0
gravatar for Tomáš Beluský
7.6 years ago by
Brno
Tomáš Beluský90 wrote:

Hi, I am implementing tool for detecting of structural variants and I am combining read pair and split read methods. The input is BAM with already mapped paired ends. When I find pair where one end is properly aligned and second is aligned with clipped sequence, I want to remap this sequence in surroundings of properly aligned end. So I need tool which can take these paired ends as input and do that for me. Or input can be clipped sequence and region where it should be mapped. So my question is if there is any tools, which can handle this. Also all other ideas are welcome. Thanks!

sequence alignment • 1.9k views
ADD COMMENTlink written 7.6 years ago by Tomáš Beluský90

I am not sure what you want but Pindel (https://trac.nbic.nl/pindel/) does exactly what you are trying to do.

ADD REPLYlink written 7.6 years ago by Ashutosh Pandey12k

Hydra and Lumpy-SV are also good @ detecting structural variation. Writing your own code is always fun, but validation and benchmarking is not.

ADD REPLYlink written 7.6 years ago by Zev.Kronenberg11k

GASV (https://code.google.com/p/gasv/) also works great. Though it doesnt use the split read method but it uses combination of mate pair discordance and read depth analysis to find structural variants but unfortunately no exact breakpoints.

ADD REPLYlink written 7.6 years ago by Ashutosh Pandey12k

You're right, but this is my master thesis ;)

ADD REPLYlink written 7.6 years ago by Tomáš Beluský90

As I mentioned before that Pindel is one of the tool. Have you read about it? Lumpy-sv is another tool. i don't think there is some tool/module which will do something specific you want.

ADD REPLYlink written 7.6 years ago by Ashutosh Pandey12k

Yes, I heard about it, but I want to detect variations by myself. All I need is remap clipped sequences. But finally I have solution. Inspired by ClipCrop, I am cutting clipped sequence with a minimal length and try to remap it with bwa on same chromosome, where read was found. Thanks everybody for your help!

ADD REPLYlink written 7.6 years ago by Tomáš Beluský90

Hi Tomas, I knew the post is very old. But can I know your solution for Remap Clipped Sequence? I am trying to remap the Clipped sequence for detecting some eccDNA from our NGS data. My strategy is exactly like yours. If I can follow some of your code to make it work on my data. That will be great help for my project! Thank you!

ADD REPLYlink written 18 months ago by Yijun Tian20
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