User: anovak

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anovak70
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Posts by anovak

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Clarification of pinch graph generation in GFA import
... I don't think it is needed anymore. I'm pulling it out in https://github.com/vgteam/vg/pull/2720. The intended way to import a GFA graph with overlaps will then be by first bluntifying it with a tool like Stark that can properly preserve the kmer space of the input graph. ...
written 5 months ago by anovak70
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Answer: A: error:[Surjector] could not identify path position of surjected alignment
... If there are actually *no* paths embedded in the graph, `vg surject` can't work. It uses the paths to define the linear coordinate space into which it is translating the mappings. If there are no paths, it doesn't know about any contigs on which the reads could be mapped in the output BAM file, and ...
written 6 months ago by anovak70
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Answer: A: Where is the documentation of libhandlegraph methods and objects
... The `vg` Docygen docs cover libhandlegraph. Handles are opaque types with no methods of their own, but the main libhandlegraph class, HandleGraph, is documented at https://vgteam.github.io/vg/classhandlegraph_1_1HandleGraph.html The edges of a handle are obtained from the `follow_edges` method on ...
written 10 months ago by anovak70
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Comment: C: No output from vg msga
... That's interesting that you don't even get the "preparing initial graph" message. Leaving out -b should be OK; it will start with the longest sequence. The very first thing msga does looks to be loading all the sequences into memory. Is your FASTA file anywhere near 128G? You should be able to run ...
written 11 months ago by anovak70
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Inferring Local Ethnicity of the Reference Genome
... I'm doing a project on reference bias, where it would be convenient to be able to assign regions of the GRCh38 reference assembly to the 1000 Genomes superpopulation(s) that they most closely resemble. If I could do this, I would be able to look for mapping bias in each region towards the superpopul ...
population reference ethnicity inferrence written 4.0 years ago by anovak70
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Answer: A: Convert from PSL to MAF
... I have written such a tool, which is available here. It requires a version of BioPython that can write MAF files, like this one, at least until this pull request or something like it is merged. ...
written 5.6 years ago by anovak70
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How are the GRC alt locus to primary assembly alignments generated?
... Since GRCh37, the reference has included alt loci, and those alt loci have come with GRC-created alignments back to the primary assembly. Those alignments are available in two formats, as described in <ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38.p2/RE ...
grc assembly alignment written 5.6 years ago by anovak70 • updated 5.5 years ago by Biostar ♦♦ 20
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Convert from PSL to MAF
... Hello, I am looking for a tool thgat can convert some PSL alignments to MAF format. Since MAF includes the sequence and PSL does not, I imagine that I would also need to provide some FASTA or 2bit files to make it work. Does such a tool exist? Or do I need to write my own? ...
psl maf conversion written 6.2 years ago by anovak70

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Popular Question 9 months ago, created a question with more than 1,000 views. For Convert from PSL to MAF
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Convert from PSL to MAF
Popular Question 3.9 years ago, created a question with more than 1,000 views. For How are the GRC alt locus to primary assembly alignments generated?

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