User: Carlos Borroto

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Carlos Borroto1.6k
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Washington Metropolitan Area
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Joined:
6 years, 9 months ago
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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

<prev • 82 results • page 1 of 9 • next >
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Answer: A: VCF Normalisation is required ?
... 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 15 days ago by Carlos Borroto1.6k
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Answer: A: Problem Downloading The Nt Database From Ncbi
... 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 3 months ago by Carlos Borroto1.6k
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Answer: A: Difference Between Picards Mergebamalignment And Mergesamfiles
... 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 9 months ago by Carlos Borroto1.6k
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... 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 12 months ago by Carlos Borroto1.6k
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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 20 months ago by Carlos Borroto1.6k
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Answer: A: How to calculate average coverage for all genes
... 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 20 months ago by Carlos Borroto1.6k
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Answer: A: Human GRCh38 and dbSNP VCF and GATK
... You problem seems to be you are using a dbSNP VCF with GRCh37 coordinates. The FTP location Pierre links in his answer has a GRCh38 version that should solve your problem. However, you should know the current GATK version is not "alt" aware yet. While mappers like BWA are and can correctly map read ...
written 21 months ago by Carlos Borroto1.6k
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Answer: A: How do I get the lengths of different regions targeted by the Nextera expanded r
... You can use a GTF with annotated intervals for the categories you want. For example this [one][1] from Ensembl. Use something like unix grep to create files for the categories you are interested. Then use [bedtools intersect][2] to get the regions of your BED file overlapping with each category GTF ...
written 21 months ago by Carlos Borroto1.6k
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Comment: C: UMI for Exome Target Sequencing
... I'm currently looking for how to do phasing with targeted sequencing data. I wonder if that's the reason you are looking into adding UMI to an exome analysis. I'll be highly interested in seeing if there are any valid answers to your question. ...
written 22 months ago by Carlos Borroto1.6k
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Answer: A: ClinVar local install
... I recommend you use [Ensembl VEP][1]. Among other many relevant things to catalog a variant as damaging, you will get `CLIN_SIG` or ClinVar significance classifier. Using VEP's web interface for small jobs will work just fine. For larger jobs and for more customizable usage you can install it locall ...
written 22 months ago by Carlos Borroto1.6k

Latest awards to Carlos Borroto

Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: Scientific Names In Blast Output And Databases
Popular Question 26 days 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?
Popular Question 9 weeks 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?
Appreciated 3 months ago, created a post with more than 5 votes. For A: FreeBayes vs GATK's HaplotypeCaller
Scholar 7 months ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Epic Question 10 months ago, created a question with more than 10,000 views. For Scientific Names In Blast Output And Databases
Epic Question 14 months ago, created a question with more than 10,000 views. For Scientific Names In Blast Output And Databases
Gold Standard 19 months ago, created a post with more than 25 bookmarks. For Which Bioinformatic Friendly Pipeline Building Framework?
Teacher 20 months 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 21 months ago, created a post with more than 5 votes. For A: Scientific Names In Blast Output And Databases
Scholar 21 months ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Great Question 22 months ago, created a question with more than 5,000 views. For Which Bioinformatic Friendly Pipeline Building Framework?
Scholar 23 months ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Good Question 23 months ago, asked a question that was upvoted at least 5 times. For Scientific Names In Blast Output And Databases
Popular Question 2.0 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?
Guru 2.1 years ago, received more than 100 upvotes.
Scholar 2.1 years ago, created an answer that has been accepted. For A: Looking for a working copy of Picard metric definitions page
Teacher 2.1 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 2.1 years ago, created a post with more than 5 votes. For A: Scientific Names In Blast Output And Databases
Teacher 2.2 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
Great Question 2.3 years ago, created a question with more than 5,000 views. For Scientific Names In Blast Output And Databases
Teacher 2.4 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
Popular Question 2.6 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?
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Scientific Names In Blast Output And Databases

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