Moderator: Brad Chapman

gravatar for Brad Chapman
Brad Chapman9.1k
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Location:
Boston, MA
Website:
http://bcbio.wordpress...
Twitter:
chapmanb
Last seen:
6 months, 2 weeks ago
Joined:
7 years, 7 months ago
Email:
c*******@50mail.com

Biologist and programmer at Harvard School of Public Health

Posts by Brad Chapman

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Comment: C: bam-readcount compilation with cmake 3.5.1 produces "list GET given empty list"
... Thanks for this pointer. As an additional data point, I ran into a similar issue in a restricted build environment for bioconda and adding perl to the environment fixes it for me. ...
written 9 months ago by Brad Chapman9.1k
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Comment: C: Is it possible to include BBMap in Bcbio-nextgen pipeline?
... For processing with sra you'll want to convert into standard fastq format using the SRA toolkit (http://www.ncbi.nlm.nih.gov/books/NBK158900/). In bcbio, you can add a custom reference genome for tuberculosis (https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#adding-custom- ...
written 22 months ago by Brad Chapman9.1k
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Answer: A: Is it possible to include BBMap in Bcbio-nextgen pipeline?
... It's possible to include it, but it would need integration work to include it as a new aligner. Documentation on writing that code is here: https://bcbio-nextgen.readthedocs.org/en/latest/contents/code.html#aligner Out of curiousity, why do you prefer BBMap over other integrated aligners in bcbio ...
written 22 months ago by Brad Chapman9.1k
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Answer: A: Genomes in a Bottle for GRCh38
... Steve is right that the Genome in a Bottle group is still working on a native 38 build of the reference. In the short term, we've been doing work on providing a Remapped/Crossmapped version that converts the 37 reference to 38 coordinates. This isn't finished as I'm not happy with the Remapping of S ...
written 2.2 years ago by Brad Chapman9.1k
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Answer: A: Tumor clonality algorithms
... We've been working on integrating clonality and heterogeneity estimation tools into bcbio (https://github.com/chapmanb/bcbio-nextgen). It's still a work in progress but we've been evaluating against internal datasets where we have external predictions of normal contamination. We've had the most succ ...
written 2.3 years ago by Brad Chapman9.1k
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Answer: A: Open Source projects to contribute to
... Shane; Welcome to bioinformatics work. It would be easier to offer suggestions with an idea of your programming background and biological interests. As a starting point, the ADAM project has a nice contributing guide, great group of folks, and the issue tracker has 'Pick Me Up!' issues which are me ...
written 2.7 years ago by Brad Chapman9.1k
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Answer: A: Exome Aggregation Consortium (ExAC) database ?
... Pierre; The source code is here: https://github.com/konradjk/exac_browser It looks like a MongoDB database and Python Flask webserver. It also builds on xBrowse: https://github.com/xbrowse/xbrowse ...
written 2.7 years ago by Brad Chapman9.1k
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Comment: C: Unbelievably rapid NGS analysis by Churchill
... The approach isn't species specific. The general idea is to find regions where we can reliably break analysis steps into chunks that are smaller than whole chromosomes and as balanced as possible. We do this in bcbio and it has been used across a wide variety of species without issues. Another tool ...
written 2.7 years ago by Brad Chapman9.1k
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Answer: A: Unbelievably rapid NGS analysis by Churchill
... This is absolutely possible, and as Devon mentioned similar to approaches we use in bcbio (https://github.com/chapmanb/bcbio-nextgen). In bcbio we haven't yet worked on single sample optimization. Practically we don't have users with a large number of idle cores and the use case of pushing through a ...
written 2.7 years ago by Brad Chapman9.1k
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Comment: C: How Can I Convert Bam/Sam To Wiggle
... You need to have the `wigToBigWig` executable available in your PATH. The script header has a bit more documentation: https://github.com/chapmanb/bcbb/blob/796cc2a1179df6f5030212fd5e7f36540351abdb/nextgen/scripts/bam_to_wiggle.py#L23 Hope this helps get it running. ...
written 3.0 years ago by Brad Chapman9.1k

Latest awards to Brad Chapman

Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Efetch And Biopython
Appreciated 12 months ago, created a post with more than 5 votes. For A: Gatk Hardyweinberg Calculation
Appreciated 14 months ago, created a post with more than 5 votes. For A: Gatk Hardyweinberg Calculation
Scholar 20 months ago, created an answer that has been accepted. For A: Exome Aggregation Consortium (ExAC) database ?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Should I Separate The Snp And Indel When Performing The Gatk Vqsr?
Appreciated 21 months ago, created a post with more than 5 votes. For A: Gatk Hardyweinberg Calculation
Appreciated 21 months ago, created a post with more than 5 votes. For A: Gatk Hardyweinberg Calculation
Scholar 2.1 years ago, created an answer that has been accepted. For A: Unbelievably rapid NGS analysis by Churchill
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Efetch And Biopython
Scholar 2.3 years ago, created an answer that has been accepted. For A: Unbelievably rapid NGS analysis by Churchill
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Should I Separate The Snp And Indel When Performing The Gatk Vqsr?
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Hypergeometric Test R/Bioconductor Result Categorization
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Gatk Hardyweinberg Calculation
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Hypergeometric Test R/Bioconductor Result Categorization
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Should I Separate The Snp And Indel When Performing The Gatk Vqsr?
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Gatk Hardyweinberg Calculation
Scholar 2.7 years ago, created an answer that has been accepted. For A: Unbelievably rapid NGS analysis by Churchill
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Should I Separate The Snp And Indel When Performing The Gatk Vqsr?
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Is There A Fast Hashing Function For Nucleotide K-Mers (Q-Grams)?
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: Efetch And Biopython
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Gatk Hardyweinberg Calculation
Scholar 2.7 years ago, created an answer that has been accepted. For A: Unbelievably rapid NGS analysis by Churchill
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Should I Separate The Snp And Indel When Performing The Gatk Vqsr?
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Convert Bam File To Fasta File
Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: Convert Bam File To Fasta File

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