User: dsmarcoantonio

Reputation:
30
Status:
New User
Location:
Brazil
Last seen:
1 year, 3 months ago
Joined:
4 years, 8 months ago
Email:
d*************@gmail.com

Posts by dsmarcoantonio

<prev • 8 results • page 1 of 1 • next >
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Comment: C: How to sort a VCF file lexicographically by chromosome number?
... Running on Debian 8 is slight different grep '^#' in.vcf > out.vcf && grep -v '^#' in.vcf | sort -k1,1 -k2,2n >> out.vcf Great solution Pierre ...
written 15 months ago by dsmarcoantonio30 • updated 4 months ago by RamRS21k
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Comment: C: Calculate the b allele frequency from a VCF file
... Indeed GT format would help. In this case: - 1/1: homozygous do ALT - AD: 2,15 . REF = 2 reads ; ALT = 15 reads According to https://www.biostars.org/p/61905/ BAF = coverage Alt / (coverage Alt + coverage Ref) BAF = 15/(2+15) = 0.8823 ...
written 23 months ago by dsmarcoantonio30
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Comment: C: How To Get Bed File Containing Exons Of Canonical Transcripts And Their Correspo
... I had the same problem. Just download again both bed from UCSC. Probably you need to wait and confirm the download. ...
written 24 months ago by dsmarcoantonio30
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Answer: A: uniqueome mappability file for EXCAVATOR-tool
... Download EXCAVATOR2: https://sourceforge.net/projects/excavator2tool/ Unpack: tar zxvf EXCAVATOR2_Package_v1.1.2.tgz cd /path/to/EXCAVATOR2_Package_v1.1.2/ doc folder contains the manual --> read it; follow instructions for R/Samtools/Bedtools/Perl Go To /path/to/EXCAVATOR2_Package_v1.1.2/lib/F77 ...
written 2.1 years ago by dsmarcoantonio30
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Comment: C: Curious about gene fusion in exome seuquencing data.
... Although RNA-Seq would improve gene-fusion finding nowadays Exome capture has evolve a lot. We use intron spanning capture in our custon-made exome and, in theory, we could also find gene-fusion in exome. It would be great a tool to find gene-fusion in exome. ...
written 2.6 years ago by dsmarcoantonio30
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Not able to filter 1000G (hg19_ALL.sites.2015_08.txt) in Annovar
... I am getting this error when using the 1000G to annotate may VCF: Scanning filter database hg19_ALL.sites.2015_08.txt...Argument & isn't numeric in numeric eq (==) at annotate_variation.pl line 2277, <DB> line ###. This error occurs in every line of the database. On line 2277 from annot ...
forum written 3.7 years ago by dsmarcoantonio30
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Answer: A: problem to download 1000genome database using ANNOVAR
... Try this: perl annotate_variation.pl -downdb -webfrom annovar --buildver hg19 1000g2014oct /humandb. Maybe the file is corrupted. Try download again. If error persist then check your administrator to see what is happen with your system. ...
written 3.8 years ago by dsmarcoantonio30
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Answer: A: Haplotype Determination With Next-Gen Data In Nuclear Families
... It seems that someone addressed this question. There is a new methodology using whole-exome to call haplotypes and look like promissor. Accurate local-ancestry inference in exome-sequenced admixed individuals via off-target sequence reais. Hu, Youna; Willer, Cristen; Zhan, Xiaowei Kang; Hyun Min;   ...
written 4.7 years ago by dsmarcoantonio30

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Popular Question 21 months ago, created a question with more than 1,000 views. For Not able to filter 1000G (hg19_ALL.sites.2015_08.txt) in Annovar

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