User: michael.d.mclellan

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Posts by michael.d.mclellan

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Where to download latest TCGA MAF files?
... Firehose hosts the latest "recommended" MAF for each TCGA tumor type. To retrieve these: $ wget http://gdac.broadinstitute.org/runs/code/firehose_get_latest.zip $ unzip firehose_get_latest.zip ./firehose_get -b -only Mutation_Packager_Oncotated_Raw_Calls Mutation_Packager_Oncotated_Calls data late ...
written 17 months ago by michael.d.mclellan110
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Answer: A: Consolidated MAF file for all cancers in TCGA
... Firehose now hosts the latest "recommended" MAF for each TCGA tumor type. To retrieve these: $ wget http://gdac.broadinstitute.org/runs/code/firehose_get_latest.zip $ unzip firehose_get_latest.zip ./firehose_get -b -only Mutation_Packager_Oncotated_Raw_Calls Mutation_Packager_Oncotated_Calls data ...
written 17 months ago by michael.d.mclellan110
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Answer: A: How to get somatic variant from TCGA vcf files
... You can start with VCF2MAF. You can alter the code to output whatever you want. It also adds VEP annotation https://github.com/ckandoth/vcf2maf Related threads: http://www.biostars.org/p/74822/ http://www.biostars.org/p/16143/#95159 http://seqanswers.com/forums/showthread.php?t=167 ...
written 17 months ago by michael.d.mclellan110
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Answer: A: TCGA 2011 Ovarian Data Germline BRCA1/2 status
... The BRCA1/2 germline variants reported in the 2011 publication were removed from the webpage on the NIH site at https://tcga-data.nci.nih.gov/docs/publications/ov_2011/ because policy revisions relabeled even single germline variants as protected data. They were originally published in Supplementa ...
written 18 months ago by michael.d.mclellan110
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Answer: A: Need clarity on the concept of germline mutations
... If you are mostly seeing mutations in DNMT3A, TET2, JAK1, ASXL1, in older individuals - these are typical markers of clonal hematopoiesis that increase with age. * http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313872/figure/F1/ * http://www.nejm.org/doi/full/10.1056/NEJMoa1409405 * http://www.nej ...
written 18 months ago by michael.d.mclellan110
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Answer: A: Amino Acid Change To Genomic Location
... http://bioinformatics.mdanderson.org/main/Transvar Introduction TransVar is a reverse annotator for inferring genomic characterization(s) of mutations (e.g., chr3:178936091 G/A) from protein or cDNA annotation(s) (e.g., PIK3CA p.E545K or PIK3CA c.1633G>A). It is designed for resolving ambiguous ...
written 20 months ago by michael.d.mclellan110
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Answer: A: Questions about BreakDancer
... It would be better to use a more descriptive subject and describe the type of data you are dealing with. To start you might read this. * Duan J, Zhang J-G, Deng H-W, Wang Y-P (2013) Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies. PLoS ONE ...
written 21 months ago by michael.d.mclellan110
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Answer: A: How to Convert SNP's that produced from Varscan into 0,1,2 ?
... WT=1 0/0 HET=1 0/1 HOM=1 1/1 NC=1 . ...
written 23 months ago by michael.d.mclellan110
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Answer: A: genome music bmr cal-covg
... Check out http://gmt.genome.wustl.edu/packages/genome-music/genome-music-bmr-calc-covg.html   --bam-list Provide a file containing sample names and normal/tumor BAM locations for each. Use the tab- delimited format [sample_name normal_bam tumor_bam] per line. Additional columns like clinical data ...
written 2.3 years ago by michael.d.mclellan110
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Answer: A: what is the covg means of the genome music bmr cal-covg
... Check out replies to 142819 and 95308 https://www.biostars.org/p/142819/ https://www.biostars.org/p/95308/ Also the online documentation at http://gmt.genome.wustl.edu/packages/genome-music/genome-music-bmr-calc-covg.html ...
written 2.3 years ago by michael.d.mclellan110

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