User: Mitch Bekritsky

gravatar for Mitch Bekritsky
Mitch Bekritsky1.2k
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Location:
London, England
Website:
http://schatzlab.cshl....
Last seen:
1 year, 3 months ago
Joined:
8 years, 5 months ago
Email:
m*****************@gmail.com

Posts by Mitch Bekritsky

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Answer: A: POS Length of 1000 genomes VCF
... Using bcftools, you should be able to do something like this without decompressing your VCF: ``` bcftools query -f "%POS\n" | awk 'NR == 1; END{print} ``` A word of warning: I haven't tried this out yet, so it might contain an error or two. ...
written 2.5 years ago by Mitch Bekritsky1.2k
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Comment: C: Difference between the two models in manta
... Have you checked the method overview or the methods PDF in the repo? Manta can run on germline only, tumor only, and paired tumor/normal subtractions. I believe it's methods PDF explains most of the details. There's also the [preprint][1] on the biorXiv, which has a pretty extensive supplement. ...
written 2.7 years ago by Mitch Bekritsky1.2k
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Comment: C: Selecting Variants based on annotations in a VCF file
... Just curious--do you want to produce a valid VCF as output, or just find the records of interest? ...
written 3.0 years ago by Mitch Bekritsky1.2k
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Answer: A: Selecting Variants based on annotations in a VCF file
... [bcftools view][1] is your friend here. I'd suggest reading the documentation on the linked page for more details, but something along the lines of bcftools view -i "ANN~MODIFIER" -o modifier.vcf -Ov init.vcf should get you a VCF file with the variants you're looking for. [1]: https://samt ...
written 3.0 years ago by Mitch Bekritsky1.2k
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Answer: A: What's the recommended graduate educational path for a fullstack developer to tr
... I work at a biotech company It really depends on what you want to do. If your focus will be primarily software engineering, then you might not need an MS or a Ph.D. As a full stack developer with some reasonably popular bioinformatics languages, you should be able to find something with the skill ...
written 3.1 years ago by Mitch Bekritsky1.2k
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Comment: C: Scalpel Error - INDELS
... Why not email the contact? ...
written 3.4 years ago by Mitch Bekritsky1.2k
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Answer: A: PCA on VCF
... Illumina has a C++ package that does partial PCA on a population VCF directly: https://github.com/Illumina/akt (In the interest of full disclosure, I work at Illumina, but do not work on this tool) ...
written 3.5 years ago by Mitch Bekritsky1.2k
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Answer: A: intersect VCF files
... [bcftools isec][1] is very easy to use. With a sample command line like bcftools isec -p isec_output -Oz 1.vcf.gz 2.vcf.gz You can get four output files in gzipped VCFs 1. `isec_output/0000.vcf.gz` would be variants unique to `1.vcf.gz` 2. `isec_output/0001.vcf.gz` would be variants unique ...
written 3.6 years ago by Mitch Bekritsky1.2k • updated 12 months ago by RamRS24k
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Comment: C: Convert BED(UCSC) to VCF
... Just curious--did you end up using either of my tweaks?  Which one ended up working for you? ...
written 4.3 years ago by Mitch Bekritsky1.2k
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Comment: C: Convert BED(UCSC) to VCF
... cmmodule is a directory within CrossMap lib that contains python modules for CrossMap.py.  I can think of two ways you can add the lib directory to your python path.  You can do it in BASH by running something like export PYTHONPATH=/home/user/CrossMap/usr/local/lib/python2.7/site-packages:$PYTHON ...
written 4.3 years ago by Mitch Bekritsky1.2k

Latest awards to Mitch Bekritsky

Teacher 24 months ago, created an answer with at least 3 up-votes. For A: The Logic Behind The Naming System In 1000Genomes Ftp Arrangements
Guru 3.0 years ago, received more than 100 upvotes.
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: The Logic Behind The Naming System In 1000Genomes Ftp Arrangements
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: Getting Unmapped Reads: Comparing Fastq To Bam
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Extract Only Uniquely Mappable Reads From Bam Files
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Extract Only Uniquely Mappable Reads From Bam Files
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: The Logic Behind The Naming System In 1000Genomes Ftp Arrangements
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Getting Unmapped Reads: Comparing Fastq To Bam
Appreciated 4.7 years ago, created a post with more than 5 votes. For A: Problem With Picard Dedup In Illumina Alignment Pipeline
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Scholar 5.1 years ago, created an answer that has been accepted. For A: I need to download a list of all human genes with their respective Esemble gene
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: The Logic Behind The Naming System In 1000Genomes Ftp Arrangements
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Popular Question 5.4 years ago, created a question with more than 1,000 views. For Reducing I/O Burden Of Bamtools C++ Api
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Problem With Picard Dedup In Illumina Alignment Pipeline
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Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Problem With Picard Dedup In Illumina Alignment Pipeline
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Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: The Logic Behind The Naming System In 1000Genomes Ftp Arrangements
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