User: hershman

gravatar for hershman
hershman40
Reputation:
40
Status:
New User
Location:
Cambridge, Boston MA, United States
Website:
www.stevehershman.com
Scholar ID:
Google Scholar Page
Last seen:
1 month, 3 weeks ago
Joined:
6 years, 4 months ago
Email:
h*******@gmail.com

Posts by hershman

<prev • 5 results • page 1 of 1 • next >
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Answer: A: CNV analysis tool on exome data for NGS
... They all suck - the data is too noisy.  The folks at the Broad claims XHMM is the best, but I didn't get great results from it.  I liked CoNIFER (was able to use it sucessfully here), but watch out - the code has a few bugs (If I remeber correctly, the depth data and probe locations can become missa ...
written 4.4 years ago by hershman40
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Comment: C: Liftover Gvf From Hg18 To Hg19
... I would but the mapped file ended up being just a header and the unmapped file had all of the lines ...
written 6.4 years ago by hershman40
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Comment: C: Liftover Gvf From Hg18 To Hg19
... I tried using the liftover tool, but it gave me a warning: WARNING: -gff is not recommended. Use 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>' ldHgGene is no longer supported and the new version of the tool (gff3ToGenePred) gives an error: Input file must conform to ...
written 6.4 years ago by hershman40
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Answer: A: How To Filter Vcf Files From 1000 Genomes Release V3.2010-11 (Alternative Source
... I was unable to find exome calls from the 1000 genomes project about a month back. One option to avoid downloading the files is to play with them on Amazon ...
written 6.4 years ago by hershman40
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Liftover Gvf From Hg18 To Hg19
... Hi, I'd like to liftover a few gvf files form hg18 to hg19. Do tools exist for this purpose? While the gvf format is supposed to be an extension of gff3, I couldn't get liftover or the gff3ToGenePred tools to accept the files. Thanks! ...
liftover hg19 written 6.4 years ago by hershman40 • updated 5.6 years ago by deanna.church1.1k

Latest awards to hershman

Popular Question 4.4 years ago, created a question with more than 1,000 views. For Liftover Gvf From Hg18 To Hg19
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: CNV analysis tool on exome data for NGS

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