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haplotype network analysis with Pegas package in R
haplotype pegas R
updated 3.7 years ago by ▴ 40 • written 5.0 years ago by ▴ 200
4
votes
5
replies
6.4k
views
VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
GATK
updated 4.1 years ago by • 0 • written 6.7 years ago by ▴ 200
0
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1
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7.0k
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Comment: C: add sample name to bam header based on bam file name
4.2 years ago by Ana ▴ 200
1
vote
1
reply
7.0k
views
Comment: C: add sample name to bam header based on bam file name
4.2 years ago by Ana ▴ 200
3
votes
5
replies
7.0k
views
add sample name to bam header based on bam file name
samtools
updated 4.2 years ago by 166k • written 4.2 years ago by ▴ 200
0
votes
0
replies
807
views
convert bam to cram with non-local reference fasta
samtools cram
4.3 years ago by Ana ▴ 200
0
votes
3
replies
8.9k
views
012 genotype matrix using vcf tools
vcftools genotype-matrix
updated 22 months ago by 45k • written 7.6 years ago by ▴ 200
1
vote
2
replies
1.6k
views
how to calculate the proportion of SNPs with DP more than 5
r depth of coverage
updated 5.4 years ago by 20 • written 7.6 years ago by ▴ 200
0
votes
0
replies
1.0k
views
how to calculate genetic position for each marker from the genetic map file?
genetic-position map
updated 2.1 years ago by 45k • written 6.0 years ago by ▴ 200
5
votes
1
reply
1.3k
views
how to assign SNPs to each gene with overlapping intervals in r?
r
updated 6.1 years ago by 36k • written 6.1 years ago by ▴ 200
3
votes
1
reply
1.9k
views
Assign a genomic region to a window
R windows bioconductor GenomicRanges
updated 6.1 years ago by 4.1k • written 6.1 years ago by ▴ 200
0
votes
2
replies
4.1k
views
How to add significance level to correlation heatmap using ggplot2
ggplot correlation r
updated 6.2 years ago by 36k • written 6.2 years ago by ▴ 200
2
votes
7
replies
4.2k
views
extract sample DP values from VCF
vcf perl vcftools
updated 22 months ago by 45k • written 8.1 years ago by ▴ 200
3
votes
1
reply
3.7k
views
difference between read depth (DP) at site (INFO) and sample(FORMAT) level
read depth vcf
updated 6.3 years ago by 12k • written 8.0 years ago by ▴ 200
4
votes
6
replies
1.7k
views
Attaching genotypes in the vcf files to individual ID
genotype
updated 6.3 years ago by 12k • written 7.0 years ago by ▴ 200
3
votes
1
reply
9.1k
views
genomic inflation factor and how to use it to estimate adjusted P-values in GWAS?
GWAS lambda
updated 6.4 years ago by ★ 3.0k • written 6.4 years ago by ▴ 200
0
votes
1
reply
2.4k
views
SNPs in high LD after LD pruning
LD SNPrelate
updated 6.6 years ago by 89k • written 6.6 years ago by ▴ 200
0
votes
0
replies
6.4k
views
Comment: C: VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
6.7 years ago by Ana ▴ 200
1
vote
2
replies
1.6k
views
tools to align DNA sequences against protein sequence
fastq alignment DNA
updated 2.1 years ago by 45k • written 6.7 years ago by ▴ 200
1
vote
0
replies
1.6k
views
hypergeometric test on outlier SNPs
outliers hypergeometric test R
6.8 years ago by Ana ▴ 200
1
vote
1
reply
1.4k
views
TukeyHSD does not match the box plot
depth of coverage anova
6.8 years ago by Ana ▴ 200
1
vote
18
replies
5.2k
views
Compute correlation for depth of coverage between 2 datasets with different length in R
depth of coverage correlation R
updated 7.0 years ago by 12k • written 7.0 years ago by ▴ 200
0
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1
reply
5.2k
views
Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
7.0 years ago by Ana ▴ 200
0
votes
1
reply
5.2k
views
Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
7.0 years ago by Ana ▴ 200
0
votes
1
reply
5.2k
views
Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
7.0 years ago by Ana ▴ 200
0
votes
1
reply
5.2k
views
Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
7.0 years ago by Ana ▴ 200
0
votes
1
reply
5.2k
views
Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
7.0 years ago by Ana ▴ 200
12
votes
29
replies
7.0k
views
compute depth of coverage for certain regions of the genome using samtools depth
depth of coverage samtools
updated 7.0 years ago by 16k • written 7.0 years ago by ▴ 200
0
votes
1
reply
1.7k
views
Comment: C: attaching genotypes in the vcf files to individual ID
7.0 years ago by Ana ▴ 200
0
votes
1
reply
1.7k
views
Comment: C: attaching genotypes in the vcf files to individual ID
7.0 years ago by Ana ▴ 200
0
votes
0
replies
2.8k
views
Comment: C: no output after running samtools depth
7.0 years ago by Ana ▴ 200
0
votes
1
reply
2.8k
views
Comment: C: no output after running samtools depth
7.0 years ago by Ana ▴ 200
2
votes
5
replies
2.8k
views
no output after running samtools depth
samtools bam
7.0 years ago by Ana ▴ 200
0
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3
replies
7.0k
views
Comment: C: compute depth of coverage for certain regions of the genome using samtools depth
7.0 years ago by Ana ▴ 200
0
votes
1
reply
7.0k
views
Answer: A: compute depth of coverage for certain regions of the genome using samtools depth
7.0 years ago by Ana ▴ 200
0
votes
1
reply
7.0k
views
Comment: C: compute depth of coverage for certain regions of the genome using samtools depth
7.0 years ago by Ana ▴ 200
0
votes
2
replies
7.0k
views
Comment: C: compute depth of coverage for certain regions of the genome using samtools depth
7.0 years ago by Ana ▴ 200
0
votes
1
reply
7.0k
views
Comment: C: compute depth of coverage for certain regions of the genome using samtools depth
7.0 years ago by Ana ▴ 200
0
votes
1
reply
7.0k
views
Comment: C: compute depth of coverage for certain regions of the genome using samtools depth
7.0 years ago by Ana ▴ 200
0
votes
1
reply
7.0k
views
Comment: C: compute depth of coverage for certain regions of the genome using samtools depth
7.0 years ago by Ana ▴ 200
4
votes
4
replies
2.1k
views
downloading 1000 genomes project bam files in the background
bam
7.0 years ago by Ana ▴ 200
0
votes
1
reply
5.1k
views
Comment: C: downloading bam files of phase 3 of 1000 genomes project
7.0 years ago by Ana ▴ 200
0
votes
1
reply
5.1k
views
Comment: C: downloading bam files of phase 3 of 1000 genomes project
7.0 years ago by Ana ▴ 200
0
votes
1
reply
5.1k
views
Comment: C: downloading bam files of phase 3 of 1000 genomes project
7.0 years ago by Ana ▴ 200
4
votes
8
replies
5.1k
views
downloading bam files of phase 3 of 1000 genomes project
1000genomes bam
updated 2.1 years ago by 45k • written 7.0 years ago by ▴ 200
0
votes
0
replies
1.1k
views
estimate population allele frequencies with EM (expectation-maximation) algorithm using R
R EM algorithm
7.0 years ago by Ana ▴ 200
2
votes
2
replies
1.3k
views
how to handle reads that mapped to multiple genes
alignment whole genome sequencing
updated 7.2 years ago by 35k • written 7.2 years ago by ▴ 200
0
votes
1
reply
2.2k
views
Comment: C: multiple DNA reads aligned to the same gene
7.2 years ago by Ana ▴ 200
0
votes
1
reply
2.2k
views
Comment: C: multiple DNA sequences aligned to the same gene
7.2 years ago by Ana ▴ 200
4
votes
5
replies
2.2k
views
multiple DNA reads aligned to the same gene
alignment protein whole genome
7.2 years ago by Ana ▴ 200
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