User: krithika.gu

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krithika.gu200
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3 months, 1 week ago
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Posts by krithika.gu

<prev • 16 results • page 1 of 2 • next >
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Answer: A: How to apply GenVisR Bioconductor package on VCF file
... Thank you for all this feedback. I did manage to convert my VCF to MAF file. But am unable to read the MAF file into my R since I have an older R version due to my Mavericks OS. So I'm trying to do a workaround with this "custom" file type. Is there an easy way to convert the MAF file format into ...
written 3 months ago by krithika.gu200
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How to apply GenVisR Bioconductor package on VCF file
... Hello, I have a VCF file and I am looking to apply the GenVisR Bioconductor package, so I can create a waterfall plot. I read the documentation and was not sure if it will accept VCF file format, or whether I need to convert the VCF into MAF or MGI . Any pointers on how to get this package workin ...
vcf R bioconductor written 3 months ago by krithika.gu200
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Comment: A: error installing samtools on ubuntu
... Here are the steps I followed to fix it. Hope this is helpful to others #Install the missing libraries sudo apt-get install libncurses-dev # repeat the "make" step. This time no error ubuntu@ubuntu:~/Documents/software/samtools-1.3$ make #create a SEPARATE FOLDER c ...
written 23 months ago by krithika.gu200
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error installing samtools on ubuntu
... Hello, I'm trying to install samtools 1.3 on my ubuntu instance. When I try "make" it get the following error I have previously installed samtools using "apt-get" pre-compiled binary, but that is such an old version, I would like to get the latest version of samtools 1.3 Could anyone help me figu ...
samtools written 23 months ago by krithika.gu200 • updated 23 months ago by Ryan Dale4.7k
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Comment: C: Is it possible to add all possible VCF annotations in one command using ANNOVAR
... Annovar groups annotations into 3 types (gene-based, region-based, filter-based) . It looks like there are 3 different commands to do various types of annotations. #region-based anno annotate_variation.pl -regionanno -buildver hg19 -dbtype cytoBand ex1.avinput humandb/ #f ...
written 23 months ago by krithika.gu200
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Is it possible to add all possible VCF annotations in one command using ANNOVAR ?
... Hello So I know Annovar documentation talks about gene-based, region-based and filter-based annotations. I am interested in annotating my input VCF file with ALL these possible annotations. Annovar documentation provides 3 different examples for gene-based, region-based and filter-based annotati ...
annovar written 23 months ago by krithika.gu200 • updated 22 months ago by Biostar ♦♦ 20
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Snpsift to filter a number of genes
... Hello, I have a VCF file, and would like to pull out all variants in various genes of interest (I have about 200 genes) I created a txt file with all my genes of interest. cat variants.vcf | java -jar SnpSift.jar filter --set input.txt "EFF[*].GENE in SET[0]" > filtered.vcf This seemed t ...
snpsift snpeff snp variant annotation written 2.3 years ago by krithika.gu200
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Looking for publicly available VCF files on cardiology
... Hello, I am looking for VCF files that have information about cardiology patients. Publicly available data would be great. The VCF file (single sample VCF for multi sample VCF) must contain variant calls for each sample I found several cardiology studies in dbGAP and SRA, but I believe dbGAP / SRA ...
vcf written 2.4 years ago by krithika.gu200
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How to find annotation file version from CDF file
... Hello, I have some .CEL files that were profiled on Affymetrix Human Genome Wide SNP 6.0 array. This was done a while back by some one else,  I am trying to back track and find out what annotation file version was used . There is a CDF File called "GenomeWideSNP_6.Full.cdf" . Is there a way to fin ...
snp affymetrix written 2.5 years ago by krithika.gu200 • updated 2.5 years ago by Maxime Lamontagne2.0k
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Comment: C: identification of viral gene from fastq or BAM file
... When you say "mapping rate" what do you mean ? When I aligned to genome using BWA, the % of alignment was > 80% ...
written 3.8 years ago by krithika.gu200

Latest awards to krithika.gu

Appreciated 20 months ago, created a post with more than 5 votes. For How to plot coverage and depth statistics of a bam file
Prophet 20 months ago, created a post with more than 20 followers. For How to plot coverage and depth statistics of a bam file
Good Question 20 months ago, asked a question that was upvoted at least 5 times. For How to plot coverage and depth statistics of a bam file
Popular Question 20 months ago, created a question with more than 1,000 views. For error installing samtools on ubuntu
Popular Question 20 months ago, created a question with more than 1,000 views. For identification of viral gene from fastq or BAM file
Epic Question 22 months ago, created a question with more than 10,000 views. For How to plot coverage and depth statistics of a bam file
Great Question 2.5 years ago, created a question with more than 5,000 views. For How to plot coverage and depth statistics of a bam file
Great Question 2.5 years ago, created a question with more than 5,000 views. For How to plot coverage and depth statistics of a bam file
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How to plot coverage and depth statistics of a bam file
Student 3.8 years ago, asked a question with at least 3 up-votes. For How to plot coverage and depth statistics of a bam file

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