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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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pindel #39

Open ghost opened 8 years ago

ghost commented 8 years ago

What does the output pindel_RP refer to ?

liangkaiye commented 8 years ago

read-pair evidence.

kaiye2016@outlook.com

From: ggg3 Date: 2016-04-20 05:54 To: genome/pindel Subject: [genome/pindel] pindel (#39) What does the output pindel_RP refer to ? — You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub

ghost commented 8 years ago

So, we look at it just to find Read-pairs ? or to confirm the outout of other pindel outputs ? Whats the significance of this file ?

On Tue, Apr 19, 2016 at 9:44 PM, Kai Ye notifications@github.com wrote:

read-pair evidence.

kaiye2016@outlook.com

From: ggg3 Date: 2016-04-20 05:54 To: genome/pindel Subject: [genome/pindel] pindel (#39) What does the output pindel_RP refer to ? — You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/39#issuecomment-212206042

liangkaiye commented 8 years ago

RP is not part of the official call sets so that we have not worked on a vcf converter. It is rather an intermediate file for us to look for split-read evidence of larger variants.

kaiye2016@outlook.com

From: ggg3 Date: 2016-04-20 22:12 To: genome/pindel CC: Kai Ye; Comment Subject: Re: [genome/pindel] pindel (#39) So, we look at it just to find Read-pairs ? or to confirm the outout of other pindel outputs ? Whats the significance of this file ?

On Tue, Apr 19, 2016 at 9:44 PM, Kai Ye notifications@github.com wrote:

read-pair evidence.

kaiye2016@outlook.com

From: ggg3 Date: 2016-04-20 05:54 To: genome/pindel Subject: [genome/pindel] pindel (#39) What does the output pindel_RP refer to ? — You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/39#issuecomment-212206042

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