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Recommended SV caller for downstream analysis #118

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amrita1983 opened this issue Feb 19, 2018 · 6 comments
Closed

Recommended SV caller for downstream analysis #118

amrita1983 opened this issue Feb 19, 2018 · 6 comments
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feature-request

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@amrita1983
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Hi,

I have aligned nanopore (1D) data using minimap2 for a human sample.
But when I am trying to use the sorted.bam of the same for SV calling in using Sniffles, its not giving any output.
I want to know what are the SV callers that I can use for minimap bam file.
@lh3
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lh3 commented Feb 19, 2018

Sniffles would be the best. I don't know why sniffles does not work with minimap2. You have to ask their developers. Sorry. BTW, for SV calling, please use the latest master. v2.8 has a bug.

@jblamyatifremer
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To amrita1983

I tried several times (with the latest version of both progs) to use sniffles on bam from minimap2 but it did not work. Maybe i miss some commands.
In the sniffles github, they recommand NGMLR aligner even if some use of -cs tag is planned on sniffles see https://github.com/lh3/minimap2#the-cs-optional-tag
Cheers

@leila0210
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Sniffles does not work with minimap2 cause no MD strings detected, so is it possible to output MD in minimap2?

@jblamyatifremer
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+1 for Leila0210.

lh3 added a commit that referenced this issue Mar 22, 2018
@lh3
r751: optionally output MD (#118)
8766d28
@lh3
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lh3 commented Mar 22, 2018

With github master, you can get the MD tag with:

minimap2 --MD

Please let me know if it works. Thank you.

@wangyugui wangyugui mentioned this issue Mar 23, 2018
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@wdecoster wdecoster mentioned this issue Mar 23, 2018
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@lh3
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lh3 commented Mar 30, 2018

In fritzsedlazeck/Sniffles#51, the Sniffles developers confirmed that Sniffles should work once minimap2 outputs the MD tag, though I haven't tested this myself. I am closing the issue. If you have problems, feel free to comment on this thread or open a new issue. Thank you.

@lh3 lh3 closed this as completed Mar 30, 2018
@lh3 lh3 mentioned this issue Apr 2, 2018
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@lh3 @jblamyatifremer @amrita1983 @leila0210