User: sutturka

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sutturka120
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USA
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Posts by sutturka

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Running vcf2maf on snpeff-annotated vcfs
... [This issue][1] on github page is very similar and comments on this issue may be helpful. [1]: https://github.com/mskcc/vcf2maf/issues/174 ...
written 22 days ago by sutturka120
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Answer: A: Issue converting VCF to MAF using snpEff annotations
... Hi, Please check the [GitHub issues][1] page which have solution for using this tool without installing VEP or use SnpEff annotated files. [1]: https://github.com/mskcc/vcf2maf/issues/160 ...
written 7 weeks ago by sutturka120
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Answer: A: Running vcf2maf on snpeff-annotated vcfs
... This is a known issue and could happen because of newer annotation types added in SnpEff. Please see the [GitHub issues][1] page for vcf2maf. [1]: https://github.com/mskcc/vcf2maf/issues?utf8=%E2%9C%93&q=Use%20of%20uninitialized%20value ...
written 7 weeks ago by sutturka120
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Comment: C: Convert (Copy Number Variation) CNV to gene
... Let me jump in and point you to [this discussion][1]. If you have confident CNV calls then you can use bedtools to get genes overlapping with CNV segments. Let's say I am fairly confident about the CNV calls. However, I am not sure if mere overlap of genes with CNV segments is enough to assign genes ...
written 7 weeks ago by sutturka120
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Comment: C: How to annotate CNV events with gene information?
... I was able to follow this approach and get the annotations for the CNVs. Essentially, I got the genes which are overlapping with CNVs and then I assigned the status (Amp/Del/Neutral) to each gene according to CNV status. However, this is a mere overlap approach and what is your opinion on directly u ...
written 7 weeks ago by sutturka120
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Comment: C: How to determine high-quality somatic mutations
... As far as I know, the latest version of Mutect within GATK4 supports somatic mutation calling without paired normals. All you need is germline SNP data (may be from dbSNP) and you can create a Panel of Normal (PON) if you have access to public data (BAM files from normal individuals sequenced with s ...
written 10 weeks ago by sutturka120
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Comment: C: mouse mm10 supporting file for GISTIC 2.0
... Did any of you find the answer how to run GISTIC for non-human data? Please share. ...
written 10 weeks ago by sutturka120
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Comment: C: gistic for whole genome sequencing copy number analysis
... I have called somatic CNVs using GATK4 on **canine (dog) data**. I have standard output from GATK which is a `seg` file as shown below ![SEG Format file][1] I am not sure how should I convert above format to GISTIC input format. Any comments would be helpful. Also, for the **markers file** [this ...
written 11 weeks ago by sutturka120
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Comment: C: How to use MutSigCV correctly
... Thank you for the pointer to CovGen. I am working on the canine data and I was able to successfully generate the MutSigCV formatted coverage file using CovGen. Do you have any directions to generate the [gene.covariates.txt](ftp://ftp.broadinstitute.org/pub/genepattern/example_files/MutSigCV_1.3/g ...
written 11 weeks ago by sutturka120
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Comment: C: MutSigCV input files
... There is a tool [CovGen][1] which can be used to generate the sample/experiment specific coverage files as required by MutSigCV. I have not used this tool yet, but I will try it soon. In the meanwhile, if you have figured out the way to run the MutSigCV, please post any suggestions which might be us ...
written 12 weeks ago by sutturka120

Latest awards to sutturka

Scholar 15 months ago, created an answer that has been accepted. For A: Career in Bioinformatics
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Career in Bioinformatics
Scholar 18 months ago, created an answer that has been accepted. For A: Career in Bioinformatics
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Career in Bioinformatics

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