User: mohesan

gravatar for mohesan
mohesan10
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10
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New User
Location:
Canada
Last seen:
2 years, 6 months ago
Joined:
2 years, 10 months ago
Email:
m********@hotmail.com

Posts by mohesan

<prev • 7 results • page 1 of 1 • next >
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Answer: A: insertion in pindel _D file?
... It turns out that they are complex events. If you used pindel2vcf to convert the pindel outputs to vcf you will be able to see both the reference and alternative alleles for that event.  ...
written 2.6 years ago by mohesan10
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Pindel Reports Deletions in various ways
... Hey I am working with the tool Pindel to analyse bwa sequenced reads for insertions and deletions.   and I realized that some of the reported deletion events look as if they should be an insertion. Pindel returns the events it finds by first outputting the line reference genome and the the aligned r ...
genome pindel alignment sequencing written 2.7 years ago by mohesan10
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Comment: A: insertion in pindel _D file?
... I have noticed the same issue. Here is an image of part of a _D file. the Deletion event are separated by a row of '#'. as you can see the first event is a deletion while the second is an insertion. but both of them are outputted to the deletion event file by pindel. I've tried running pindel multip ...
written 2.8 years ago by mohesan10
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Comment: C: What are the rules Pindel uses to determine which pairs of reads it will use?
... Majority of the reads that Pindel did not use were mapped in proper pair ...
written 2.8 years ago by mohesan10
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Comment: C: What are the rules Pindel uses to determine which pairs of reads it will use?
... I am not sure. Is that a possible reason for them to remove reads? ...
written 2.8 years ago by mohesan10
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Comment: C: What are the rules Pindel uses to determine which pairs of reads it will use?
... For example should there be a certain MS score(i doubt this is the case)? ...
written 2.8 years ago by mohesan10
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What are the rules Pindel uses to determine which pairs of reads it will use?
... I am trying to determine how Pindel decides on which (pair)reads it uses to analyse for structural variances. Pindel takes in a bam file that has been aligned using BWA. Pindel then applies the pattern-growth method,to find indels, on reads that could not be mapped but their pair was mapped successf ...
genome alignment sequence tool pindel written 2.8 years ago by mohesan10

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