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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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Version 0.2.5b8 OUTPUT interpreting #28

Open Czh3 opened 8 years ago

Czh3 commented 8 years ago

How do I interpret the outputs of Pindle(verion 0.2.5b8). It's different from former version. eg.:

0 D 1 NT 0 "" ChrID MT BP 317 319 BP_range 317 326 Supports 9 9 + 6 6 - 3 3 S1 28 SUM_MS 540 2 NumSupSamples 2 2 W-20G 4465 4465 4 4 1 1 W-C 2939 2939 2 2 2 2

The last few columns "W-20G 4465 4465 4 4 1 1 W-C 2939 2939 2 2 2 2", what "4465" means? 4465 reads mapping upstream of the Deletion?

Thanks in advance!

liangkaiye commented 8 years ago

the two big numbers are reads supporting the reference allele.

On 1/1/16 3:08 PM, Czh3 wrote:

How do I interpret the outputs of Pindle(verion 025b8) It's different from former version eg: #################################################################################################### 0 D 1 NT 0 "" ChrID MT BP 317 319 BP_range 317 326 Supports 9 9 + 6 6

  • 3 3 S1 28 SUM_MS 540 2 NumSupSamples 2 2 W-20G 4465 4465 4 4 1 1 W-C 2939 2939 2 2 2 2

The last few columns "W-20G 4465 4465 4 4 1 1 W-C 2939 2939 2 2 2 2", what "4465" means? 4465 reads mapping upstream of the Deletion?

Thanks in advance!

— Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/28.

Czh3 commented 8 years ago

Thanks Kai, That's what I need. Is there the information(reads supporting reference allele) in Large Insertion(LI), I really want to know the mutation frequency. Thanks again!

liangkaiye commented 8 years ago

LI is not well implemented. so that the efficiency of detection is unknown.

On 1/1/16 11:06 PM, Czh3 wrote:

Thanks Kai, That's what I need. Is there the information in Large Insertion(LI), I really want to know the mutation frequency. Thanks again!

— Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/28#issuecomment-168312403.

Czh3 commented 8 years ago

Thanks a lot ~