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Showing :
answers
3
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0
replies
417
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Answer:
Answer: Detecting somatic variants in non-tumor tissue without normals
5 months ago by
Cyriac Kandoth
6.0k
4
votes
0
replies
514
views
Answer:
Answer: How to identify whether the sample is from only one person and whether the sampl
14 months ago by
Cyriac Kandoth
6.0k
0
votes
0
replies
3.1k
views
Answer:
Answer: Understanding VCF abbreviations
17 months ago by
Cyriac Kandoth
6.0k
5
votes
2
replies
12k
views
Answer:
Answer: Best Hardware Solution For Medium-Size Bioinformatics Lab [15-20 Computers]
20 months ago by
Cyriac Kandoth
6.0k
5
votes
1
reply
3.1k
views
Answer:
Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
2.5 years ago by
Cyriac Kandoth
6.0k
3
votes
1
reply
2.2k
views
Answer:
Answer: Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data?
2.7 years ago by
Cyriac Kandoth
6.0k
3
votes
1
reply
4.4k
views
Answer:
Answer: Good annotation databases for a VCF file (somatic variants)
2.9 years ago by
Cyriac Kandoth
6.0k
3
votes
1
reply
5.2k
views
Answer:
Answer: How to convert maf to vcf while retaining original mutation notations?
3.0 years ago by
Cyriac Kandoth
6.0k
4
votes
0
replies
6.9k
views
Answer:
A: Doesn't Base Quality Score Recalibration degrade sensitivity in heavily mutated
3.2 years ago by
Cyriac Kandoth
6.0k
0
votes
1
reply
5.3k
views
Answer:
A: Aggregate multiple VCFs into a single MAF or generate a multi-sample MAF from a
3.4 years ago by
Cyriac Kandoth
6.0k
2
votes
0
replies
7.2k
views
Answer:
A: Strelka Indel Allele Counts
updated 4.3 years ago by
Ram
43k • written 10.0 years ago by
Cyriac Kandoth
6.0k
5
votes
1
reply
9.5k
views
Answer:
A: How To Use Maf Files In The Absolute Software
updated 4.4 years ago by
Ram
43k • written 10.2 years ago by
Cyriac Kandoth
6.0k
3
votes
0
replies
2.5k
views
Answer:
A: MuSiC original files for testing/ MAF, rois and soo on
updated 4.4 years ago by
Ram
43k • written 8.4 years ago by
Cyriac Kandoth
6.0k
0
votes
1
reply
5.0k
views
Answer:
A: TCGA somatic mutation
updated 4.4 years ago by
Ram
43k • written 8.5 years ago by
Cyriac Kandoth
6.0k
0
votes
0
replies
3.0k
views
Answer:
A: dn/ds ratio for somatic mutation
updated 4.5 years ago by
Ram
43k • written 8.5 years ago by
Cyriac Kandoth
6.0k
1
vote
0
replies
6.2k
views
Answer:
A: TCGA Tumor matched Normal and Normal matched Tumor do not have the same number o
updated 4.5 years ago by
Ram
43k • written 8.5 years ago by
Cyriac Kandoth
6.0k
2
votes
1
reply
2.9k
views
Answer:
A: TCGA Mutation Annotation Files (MAFs) with ref_context column
updated 4.5 years ago by
Ram
43k • written 8.8 years ago by
Cyriac Kandoth
6.0k
4
votes
2
replies
2.8k
views
Answer:
Answer: Compendium of validated somatic variant calls with associated reads and referenc
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Cyriac Kandoth
6.0k
2
votes
1
reply
7.2k
views
Answer:
A: How can I convert a tab delemeted file to vcf format using vcf-annotate tool?
updated 4.6 years ago by
Ram
43k • written 9.5 years ago by
Cyriac Kandoth
6.0k
2
votes
1
reply
6.3k
views
Answer:
Answer: Finding significant overlap of mutations in a specific cancer tumors and its rep
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
Cyriac Kandoth
6.0k
11
votes
3
replies
11k
views
Answer:
A: problems with MAF for MutSigCV (vcf2maf)
updated 4.6 years ago by
Ram
43k • written 9.7 years ago by
Cyriac Kandoth
6.0k
3
votes
0
replies
5.0k
views
Answer:
A: annotating MAF files
updated 4.6 years ago by
Ram
43k • written 9.8 years ago by
Cyriac Kandoth
6.0k
1
vote
1
reply
4.1k
views
Answer:
A: Inferring zygosity information from MAF
updated 4.6 years ago by
Ram
43k • written 9.8 years ago by
Cyriac Kandoth
6.0k
3
votes
1
reply
5.0k
views
Answer:
A: Best Reference Sequence For Music And "Bit_Test" Error
updated 4.6 years ago by
Ram
43k • written 10.6 years ago by
Cyriac Kandoth
6.0k
2
votes
0
replies
5.0k
views
Answer:
A: Karyotypically Sorted Genome Assembly
updated 4.6 years ago by
Ram
43k • written 10.5 years ago by
Cyriac Kandoth
6.0k
4
votes
1
reply
2.7k
views
Answer:
A: Are There Any Caveats When Creating A Maf File For Music?
updated 5.3 years ago by
Ram
43k • written 10.6 years ago by
Cyriac Kandoth
6.0k
2
votes
1
reply
4.1k
views
Answer:
Answer: List of genes sequenced in genome sequencing data from TCGA
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Cyriac Kandoth
6.0k
19
votes
1
reply
27k
views
Answer:
Answer: Human dna reference file with no prefix 'chr'
23 months ago by
Cyriac Kandoth
6.0k
3
votes
1
reply
27k
views
Answer:
Answer: Converting Vcf File To Maf
updated 3.1 years ago by
Ram
43k • written 10.4 years ago by
Cyriac Kandoth
6.0k
8
votes
1
reply
8.5k
views
Answer:
A: From TCGA to GDC (Genomic data commons)
6.5 years ago by
Cyriac Kandoth
6.0k
1
vote
1
reply
3.6k
views
Answer:
A: Getting 1000 Genomes phase one MAF values
6.6 years ago by
Cyriac Kandoth
6.0k
2
votes
2
replies
6.0k
views
Answer:
Answer: How to get minor allele frequency of a list of variants; for example NM_004401 (
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Cyriac Kandoth
6.0k
1
vote
1
reply
3.7k
views
Answer:
A: Installing ensembl 86 VEP and vcf2maf and getting SNP MAFs
6.7 years ago by
Cyriac Kandoth
6.0k
8
votes
2
replies
12k
views
Answer:
A: Variant allele frequency in TCGA and ICGC
6.7 years ago by
Cyriac Kandoth
6.0k
5
votes
0
replies
2.5k
views
Answer:
A: Where is the pathogenicity in TCGA MAF files?
7.4 years ago by
Cyriac Kandoth
6.0k
3
votes
1
reply
3.0k
views
Answer:
A: Selecting TCGA samples by barcode in CG Hub
7.5 years ago by
Cyriac Kandoth
6.0k
2
votes
1
reply
2.9k
views
Answer:
A: genome version in cbioportal
7.5 years ago by
Cyriac Kandoth
6.0k
8
votes
3
replies
11k
views
Answer:
Answer: TCGA CNV Files
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
Cyriac Kandoth
6.0k
5
votes
0
replies
2.7k
views
Answer:
A: TCGA data: CNV SNP 6.0 vs LowPass DNAseq
7.8 years ago by
Cyriac Kandoth
6.0k
5
votes
0
replies
7.3k
views
Answer:
A: TCGA VCF & MAF content
7.8 years ago by
Cyriac Kandoth
6.0k
1
vote
0
replies
3.2k
views
Answer:
A: Mismatch in exome capture and mapping reference assembly in TCGA WXS data ?
7.9 years ago by
Cyriac Kandoth
6.0k
3
votes
0
replies
4.0k
views
Answer:
A: Vcf Statistics Given A Gff3 Annotation
8.1 years ago by
Cyriac Kandoth
6.0k
4
votes
1
reply
2.8k
views
Answer:
A: Are there recommended steps if MuSiC reports too many significantly mutated gene
8.1 years ago by
Cyriac Kandoth
6.0k
4
votes
0
replies
2.0k
views
Answer:
Answer: Tool/algorithm to assess the effect of several mutations
updated 21 months ago by
Ram
43k • written 8.2 years ago by
Cyriac Kandoth
6.0k
1
vote
0
replies
2.1k
views
Answer:
A: Is it possible to get seq data for cancers via database?
8.4 years ago by
Cyriac Kandoth
6.0k
4
votes
1
reply
2.5k
views
Answer:
Answer: Are there certain mutations ubiquitous in ALL cancers?
updated 21 months ago by
Ram
43k • written 8.4 years ago by
Cyriac Kandoth
6.0k
11
votes
1
reply
23k
views
Answer:
Answer: Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
Cyriac Kandoth
6.0k
1
vote
1
reply
2.7k
views
Answer:
Answer: TCGA 2011 Ovarian Data Germline BRCA1/2 status
updated 20 months ago by
Ram
43k • written 8.6 years ago by
Cyriac Kandoth
6.0k
1
vote
1
reply
1.8k
views
Answer:
A: Genome MuSic Mutation Relation RUntimes
8.7 years ago by
Cyriac Kandoth
6.0k
2
votes
1
reply
8.7k
views
Answer:
Answer: MAF (minor allele frequency) calculation for finding rare variants from TCGA
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
Cyriac Kandoth
6.0k
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