User: liangkaiye

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liangkaiye250
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2 years, 9 months ago
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5 years, 5 months ago
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Posts by liangkaiye

<prev • 31 results • page 1 of 4 • next >
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Answer: A: Does Pindel generate genotypes?
... there is one pindel2vcf binary inside Pindel package to convert Pindel calls to genotyped vcf.  ...
written 2.8 years ago by liangkaiye250
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Comment: A: Problem for pindel2vcf to create VCF file from pindel created _D files
... can you communicate with me by email on this? kye@genome.wustl.edu I need the pindel output lines causing the error.  ...
written 2.8 years ago by liangkaiye250
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Answer: A: What are the rules Pindel uses to determine which pairs of reads it will use?
... when you say Pindel does not use these reads, what kind of the reads you are referring to? Is it discordant read pair or the other type of difficult-to-map reads?     ...
written 2.8 years ago by liangkaiye250
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Answer: A: pindel2vcf output VCF file format
... the format is compatible with with higher VCF versions. ...
written 2.8 years ago by liangkaiye250
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Answer: A: Pindel too slow. How to speedup
... Newest Pindel code? You could split by smaller segments (say 10MB) per job with 4 cores and this will not affect interchr prediction.    If on exome data, I sometimes saw coverage spikes (several kx) in several narrow regions, this causes Pindel to slow down and have memory issue. You might use -J ...
written 2.8 years ago by liangkaiye250
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Answer: A: question about pindel
... you can directly use bam as input, -i config.   Kai ...
written 3.0 years ago by liangkaiye250
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Answer: A: Pindel segmentation fault in GetRealStart4Deletion
... can you check out the latest version at github, version "Pindel version 0.2.5a7, July 24 2014"? I should have removed the bug.  ...
written 3.2 years ago by liangkaiye250
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Answer: A: problems with pindel2vcf output
... are you using the same reference build to run Pindel2vcf? can you update your pindel to the latest version? ...
written 3.2 years ago by liangkaiye250
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Comment: C: Pindel And Mac Os X
... please use samtools 0.1.18. 0.1.19 does not work for Pindel. You need to download samtools source code and make.   on mac, you need to have gcc installed and set up properly. please fellow the instruction at http://www.ficksworkshop.com/blog/14-coding/65-installing-gcc-on-mac to download gcc and i ...
written 3.3 years ago by liangkaiye250
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Answer: A: SUM_MS field in Pindel, and unique supporting reads discrepancy
... sum of mapping quality of all supporting reads. Can you tell me the Pindel version? we have a fix in the past.   Kai ...
written 3.4 years ago by liangkaiye250

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Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Pindel And Multiple Insert Size Libraries Per Bam File

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