User: Carlos Borroto
Carlos Borroto • 1.9k
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Masters in Bioinformatics with strong focus in computational genomics and gene expression analysis. Bioinformatics Analyst with over seven years of experience in international and domestic laboratory environments. Extensive experience in computational applications for laboratory data analyses.
Specialties:Bioinformatics, UNIX/Linux administration, Molecular Biology, Cell Biology.
Posts by Carlos Borroto
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3
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1.2k
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Answer:
A: Alternative to VEP.
... I recently started playing with [Jannovar][1] and I'm pleasantly surprised how easy it has been to get up and running with it. Highly recommend giving it a try.
[1]: https://github.com/charite/jannovar/ ...
written 22 months ago by
Carlos Borroto • 1.9k
3
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1
answer
475
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1
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... All inputs for the step have to be available. See [this][1], look for bullet point "Instead of scattering separate steps, prefer to scatter over a subworkflow."
[1]: https://doc.arvados.org/user/cwl/cwl-style.html ...
written 23 months ago by
Carlos Borroto • 1.9k
0
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15k
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... This is most likely the case where you are using a `pip` command associated with a different `python` installation.
Please share the exact command used to install `pysam`. That could help decide what to do next to figure out where `pysam` might be getting installed. ...
written 2.2 years ago by
Carlos Borroto • 1.9k
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5 follow
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... I'm getting started writing CWL tools and workflows. I would like to get a good testing framework setup from the beginning. Is there something that can help testing CWL? How are you testing CWL?
I saw [cwltest][1] exists. However, the documentation is very sparse. I haven't figured out what should ...
written 2.4 years ago by
Carlos Borroto • 1.9k
• updated
2.2 years ago by
ionox0 • 360
3
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1.6k
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... 1) Yes, you do need to do normalization of the VCF, however the tools below will help you with that.
2) The main tools I know of are Illumina's [hap.py][1] and Real Time Genomics' [vcfeval][2]. Both are tools recommended by the PrecicionFDA [Truth Challenge][3].
[1]: https://github.com/Illumina ...
written 2.5 years ago by
Carlos Borroto • 1.9k
0
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2
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3.5k
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2
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... In case someone finds this thread while searching for this issue, you can ask update_blastdb to use passive mode.
$ update_blastdb --passive --decompress nt ...
written 2.8 years ago by
Carlos Borroto • 1.9k
1
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2
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7.1k
views
2
answers
... Long detailed explanation from the [GATK forum][1].
> 3C. Restore altered data and apply & adjust meta information using MergeBamAlignment
>MergeBamAlignment is a beast of a tool, so its introduction is longer. It does more than is implied by its name. Explaining these features requires ...
written 3.3 years ago by
Carlos Borroto • 1.9k
0
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1
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14k
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1
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... How do you think this will affect reads coming from two almost identical regions but for a few bases? For example SMN1/SMN2 have regions that are only differentiated by 1 base. Would `clumpify.sh` with the recommended allowed subs parameter remove non-duplicated reads for these two regions?
--Carlo ...
written 3.5 years ago by
Carlos Borroto • 1.9k
1
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0
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2.2k
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0
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Comment:
C: Rsync and python for ftp.ncbi
... I think you are falling in the trap of the [XY problem][1]. Please tell us more about what you are trying to do. Even without the details of what you really want to do, I doubt you need to get python involved here, most probably rsync by itself can do it.
[1]: http://meta.stackexchange.com/quest ...
written 4.1 years ago by
Carlos Borroto • 1.9k
2
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3
answers
4.1k
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3
answers
... I recently found myself looking for the exact info. I too decided to go with bedtools. This is my final one liner assuming a pre-sorted bam file.
bedtools coverage -sorted -d -g human_g1k_v37.genome -a genes.bed -b my_sorted.bam \
| sort -k4,4 \
| bedtools groupby -g 4 -c 8 -o mean ...
written 4.2 years ago by
Carlos Borroto • 1.9k
Latest awards to Carlos Borroto
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14 months ago,
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For A: Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
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For A: Looking for a working copy of Picard metric definitions page
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For Scientific Names In Blast Output And Databases
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For Is There A Way To Start From 454'S ".Fna" And ".Qual" Files In Gkno?
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For Is There A Way To Start From 454'S ".Fna" And ".Qual" Files In Gkno?
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For A: FreeBayes vs GATK's HaplotypeCaller
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For A: Looking for a working copy of Picard metric definitions page
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For Scientific Names In Blast Output And Databases
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3.6 years ago,
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For In Gkno'S Fastq-Vcf Pipeline, Can I Write To Disk An Intermediary Bam Aligment Currently Sent To The Stream?
Epic Question
3.6 years ago,
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For Scientific Names In Blast Output And Databases
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4.1 years ago,
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For Which Bioinformatic Friendly Pipeline Building Framework?
Teacher
4.2 years ago,
created an answer with at least 3 up-votes.
For A: Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
Appreciated
4.2 years ago,
created a post with more than 5 votes.
For A: Scientific Names In Blast Output And Databases
Scholar
4.2 years ago,
created an answer that has been accepted.
For A: Looking for a working copy of Picard metric definitions page
Great Question
4.4 years ago,
created a question with more than 5,000 views.
For Which Bioinformatic Friendly Pipeline Building Framework?
Scholar
4.4 years ago,
created an answer that has been accepted.
For A: Looking for a working copy of Picard metric definitions page
Good Question
4.4 years ago,
asked a question that was upvoted at least 5 times.
For Scientific Names In Blast Output And Databases
Popular Question
4.5 years ago,
created a question with more than 1,000 views.
For Is There A Way To Start From 454'S ".Fna" And ".Qual" Files In Gkno?
Scholar
4.5 years ago,
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For A: Looking for a working copy of Picard metric definitions page
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4.5 years ago,
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