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Correcting variant allele fraction using tumor purity (experimentally measured)
variant calling sequencing cancer SNP next-gen
4.9 years ago by Luca Beltrame ▴ 250
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7.0k
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Comment: C: Aggregate multiple VCFs into a single MAF or generate a multi-sample MAF from a
4.9 years ago by Luca Beltrame ▴ 250
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3
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7.0k
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Aggregate multiple VCFs into a single MAF or generate a multi-sample MAF from a multi-sample VCF
sequencing file-formats maf conversion
updated 4.9 years ago by 6.1k • written 8.4 years ago by ▴ 250
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0
replies
863
views
Generate coordinates of specific length between two BED features
bed bedtools
5.4 years ago by Luca Beltrame ▴ 250
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0
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1.4k
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Comment: C: Merge regions in a BED but only if they share the same value (copy number) in a
5.8 years ago by Luca Beltrame ▴ 250
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2
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1.4k
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Merge regions in a BED but only if they share the same value (copy number) in a column
bedtools copy number bedops
updated 5.8 years ago by 89k • written 5.8 years ago by ▴ 250
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6.1k
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Comment: C: Loess Normalization And Scale Issues
updated 7.2 years ago by 45k • written 14.3 years ago by ▴ 250
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4
replies
6.1k
views
Loess Normalization And Scale Issues
microarray r data
updated 7.2 years ago by 45k • written 14.3 years ago by ▴ 250
1
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0
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3.6k
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Proper way to plot VCF files from structural variant callers
sequencing visualization circos
9.5 years ago by Luca Beltrame ▴ 250
2
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4
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3.1k
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Calculation Of Theoretical Minimum Coverage Per Mutation Frequency
mutation sequencing coverage
updated 2.7 years ago by 45k • written 12.8 years ago by ▴ 250
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2
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6.5k
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Comment: C: Targeted NGS: amplicon length vs read length
9.6 years ago by Luca Beltrame ▴ 250
4
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7
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6.5k
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Targeted NGS: amplicon length vs read length
sequencing next-gen amplicon
updated 9.6 years ago by 48k • written 9.6 years ago by ▴ 250
8
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3
replies
5.8k
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Re-Annotating An Existing Gff File?
gff annotation
updated 10.1 years ago by 20 • written 13.0 years ago by ▴ 250
4
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2
replies
4.3k
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How To Interpret Dp Fields For Samples In Vcf Files?
vcf sequencing
updated 10.2 years ago by 20 • written 12.5 years ago by ▴ 250
4
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8
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5.1k
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How To Represent Two Different Indels At The Same Position In A Multisample Vcf?
vcf variant-calling sequencing
updated 11.5 years ago by 20 • written 12.1 years ago by ▴ 250
3
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4
replies
7.4k
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Build Phylogenetic Trees From Bam Files
sequencing bam
updated 11.7 years ago by ▴ 500 • written 11.9 years ago by ▴ 250
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2
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4.2k
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Comment: C: Quality Control Software For Targeted Sequencing?
11.8 years ago by Luca Beltrame ▴ 250
5
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5
replies
4.2k
views
Quality Control Software For Targeted Sequencing?
ngs analysis sequencing software
updated 11.8 years ago by 24k • written 11.8 years ago by ▴ 250
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1
reply
7.4k
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Comment: C: Build Phylogenetic Trees From Bam Files
11.9 years ago by Luca Beltrame ▴ 250
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0
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6.2k
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Comment: C: Snp Calling Of Tcga Data Using Samtools
11.9 years ago by Luca Beltrame ▴ 250
5
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5
replies
6.8k
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Convert Cds-Based Coordinate To Genomic Coordinates
genome mapping
updated 12.0 years ago by 24k • written 12.0 years ago by ▴ 250
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0
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6.8k
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Comment: C: Convert Cds-Based Coordinate To Genomic Coordinates
12.0 years ago by Luca Beltrame ▴ 250
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0
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6.8k
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Comment: C: Convert Cds-Based Coordinate To Genomic Coordinates
12.0 years ago by Luca Beltrame ▴ 250
0
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0
replies
5.1k
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Comment: C: How To Represent Two Different Indels At The Same Position In A Multisample Vcf?
12.1 years ago by Luca Beltrame ▴ 250
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0
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5.1k
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Comment: C: How To Represent Two Different Indels At The Same Position In A Multisample Vcf?
12.1 years ago by Luca Beltrame ▴ 250
1
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1
reply
5.1k
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Comment: C: How To Represent Two Different Indels At The Same Position In A Multisample Vcf?
12.1 years ago by Luca Beltrame ▴ 250
0
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1
reply
5.1k
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Comment: C: How To Represent Two Different Indels At The Same Position In A Multisample Vcf?
12.1 years ago by Luca Beltrame ▴ 250
5
votes
6
replies
4.5k
views
6 follow
Visualization Tools For Ngs Analysis Results, Suitable For Biologists
software ngs visualization variant-calling
updated 12.1 years ago by ★ 2.2k • written 12.1 years ago by ▴ 250
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0
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9.2k
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Comment: C: Finding The Number Of Reads Which Support A Variant In Vcf
12.4 years ago by Luca Beltrame ▴ 250
5
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5
replies
9.2k
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Finding The Number Of Reads Which Support A Variant In Vcf
vcf sequencing variant-calling depth-of-coverage
updated 12.4 years ago by 22k • written 12.4 years ago by ▴ 250
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0
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3.3k
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Answer: A: Bioconductor Rankprod Strange Results.
12.4 years ago by Luca Beltrame ▴ 250
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0
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6.6k
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Comment: C: Targeted Sequencing - Calculating The Minimum Exon Coverage
13.0 years ago by Luca Beltrame ▴ 250
0
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1
reply
6.6k
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Comment: C: Targeted Sequencing - Calculating The Minimum Exon Coverage
13.0 years ago by Luca Beltrame ▴ 250
0
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0
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6.6k
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Comment: C: Targeted Sequencing - Calculating The Minimum Exon Coverage
13.0 years ago by Luca Beltrame ▴ 250
4
votes
8
replies
6.6k
views
Targeted Sequencing - Calculating The Minimum Exon Coverage
sequencing coverage exon
updated 13.0 years ago by 27k • written 13.0 years ago by ▴ 250
0
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1
reply
3.9k
views
Sequencing Depth And Mutation Frequency
sequencing cancer ion-torrent depth-of-coverage
updated 13.3 years ago by 13k • written 13.4 years ago by ▴ 250
0
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1
reply
3.4k
views
How To Handle Reads Ending With Deletions In Gatk?
gatk indel analysis alignment ion-torrent
13.5 years ago by Luca Beltrame ▴ 250
8
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6
replies
13k
views
Color Clustering Results Basing On Sample Classes In R
r microarray clustering
updated 13.8 years ago by 5.2k • written 13.8 years ago by ▴ 250
0
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0
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13k
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Comment: C: Color Clustering Results Basing On Sample Classes In R
13.8 years ago by Luca Beltrame ▴ 250
0
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0
replies
13k
views
Comment: C: Color Clustering Results Basing On Sample Classes In R
13.8 years ago by Luca Beltrame ▴ 250
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