User: nilesh.gardi2688

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Posts by nilesh.gardi2688

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Varscan2 mutational calling analysis
... Hello, I have basic question in varscan2 mutation calling. varscan2 divide total SNPs into germline, somatic, LOH and unknown based on allele frequency. My question is if all 3 genomes (i.e. hg19, blood and tumor) have different nucleotide (at same position), where do that SNP should be classify? Fo ...
next-gen written 15 months ago by nilesh.gardi26880 • updated 9 months ago by Biostar ♦♦ 20
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Genotype information required in Clonality analysis using Pyclone
... I have affymetrix SNP array data and exome data for same tumor samples. I want to run Pyclone for clonal evolution experiment. I identified somatic mutations in each tumor samples using varscan2. As per Pyclone requirement, I need to input these mutations along with parental copy number informat ...
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Answer: A: I need allele copy number information for running PyClone
... How to infer allele specific copy number from DNAcopy package output or any SNP array segmentation data? I also need to run Pyclone for which I need allele specific copy number. I have exome data as well affymetrix SNP array data for same samples. ...
written 16 months ago by nilesh.gardi26880
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Answer: A: converting varscan2 output to sequenza
... Is problem get solved? I am also getting similar error as follows: Error: Error in `[.data.frame`(varscan.somatic, idx, c("ref", "var")) : undefined columns selected I am using ##fileformat=VCFv4.1 as input. Please help. ...
written 16 months ago by nilesh.gardi26880

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