User: krithika.gu
krithika.gu • 230
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Posts by krithika.gu
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Answer:
A: TCGA data on cloud
... So the NCI-GDC is the official repository of the TCGA data. They have raw and processed data. They also run best practices pipelines on the raw data, and provide processed data. Check this site out first: **https://portal.gdc.cancer.gov/** If the pipeline you want to run is the usual processing pipe ...
written 19 days ago by
krithika.gu • 230
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... Hey, I tried to use all these packages, I was able to convert VCF to MAF using https://github.com/mskcc/vcf2maf,
but they did not give me the right answer. From my understanding, these packages work well only if you have a smaller filtered VCF file of somatic mutations. If you use the original VCF ...
written 12 weeks ago by
krithika.gu • 230
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... 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 6 months ago by
krithika.gu • 230
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... 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 ...
written 6 months ago by
krithika.gu • 230
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... 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 2.2 years ago by
krithika.gu • 230
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... 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 ...
written 2.2 years ago by
krithika.gu • 230
• updated
2.2 years ago by
Ryan Dale ♦ 4.7k
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... 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 2.2 years ago by
krithika.gu • 230
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... 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 ...
written 2.2 years ago by
krithika.gu • 230
• updated
2.1 years ago by
Biostar ♦♦ 20
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... 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 ...
written 2.5 years ago by
krithika.gu • 230
1
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... 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 ...
written 2.7 years ago by
krithika.gu • 230
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