User: Jts

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Jts1.2k
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Posts by Jts

<prev • 27 results • page 1 of 3 • next >
11
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Answer: A: How To Generate The Graph Of The Genotype Space?
... In such a graph for n genotypes you have a vertex for all possible 2^n binary strings. Edges connect vertices that have a hamming distance of 1. This is the hamming graph H(n, 2). To generate such a graph, start by making a vertex for all 2^n binary strings. Then for each vertex you can generate th ...
written 7.4 years ago by Jts1.2k
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Comment: C: Should We Attempt To Redefine The Cigar String In Sam/Bam Format?
... @Michael I know samtools will handle X/= but I do not know about other tools. ...
written 7.5 years ago by Jts1.2k
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Comment: C: Should We Attempt To Redefine The Cigar String In Sam/Bam Format?
... @Istvan my argument is not that it is too expensive to store that information but that you shouldn't be forced to store it. ...
written 7.5 years ago by Jts1.2k
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Answer: A: Should We Attempt To Redefine The Cigar String In Sam/Bam Format?
... I don't think this is a good idea. BAM is designed to be a compact representation with minimal data redundancy. If you require the mismatching bases are encoded in the CIGAR string, you will pay a cost of 4 bytes for every base calling error and SNP in your data set. This is a huge cost to pay for i ...
written 7.5 years ago by Jts1.2k
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Comment: C: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
... You have an extra hypen at the end of the first link ...
written 7.6 years ago by Jts1.2k
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Answer: A: Parallel Bzip2 In Abyss
... When a bz2 file is given to abyss, the first stage of the assembler makes a call out to bunzip2 and reads the result from a pipe. The decompressed file is not stored on disk. If you are interested in testing out pbzip2 instead of bzip2, the relevant code is in function zcatExec, in Common/Uncompress ...
written 7.6 years ago by Jts1.2k
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Comment: C: Genotype Likelihood Calculation In Samtools Is Wrong?
... If you have not seen it, this paper by Heng Li gives additional/updated details on the samtools model http://bioinformatics.oxfordjournals.org/content/early/2011/09/08/bioinformatics.btr509.short ...
written 7.8 years ago by Jts1.2k
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Comment: C: Genotype Likelihood Calculation In Samtools Is Wrong?
... If you have not seen it, you might be interested in this paper by Heng Li with more/updated details on the samtools model: http://biostar.stackexchange.com/questions/12527/genotype-likelihood-calculation-in-samtools-is-wrong ...
written 7.8 years ago by Jts1.2k
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Comment: C: Read Generator With Clear Annotation Of Read Origin And Mutations
... Well, if such software doesn't exist SimSeq would be a good place to start. Alternatively, you could run samtools calmd on the SimSeq output with the original reference to fill in the MD tag. ...
written 8.0 years ago by Jts1.2k
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Answer: A: Read Generator With Clear Annotation Of Read Origin And Mutations
... John St John's SimSeq program outputs the sampled reads as a SAM file, which would provide you with the position and orientation. I don't think it tracks the position of introduced errors but it would not be too difficult to change the code to write this information as an MD tag. https://github.com/ ...
written 8.0 years ago by Jts1.2k

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