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3.4k
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haplotype network analysis with Pegas package in R
haplotype pegas R
updated 3.3 years ago by ▴ 40 • written 4.6 years ago by ▴ 200
4
votes
5
replies
6.1k
views
VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
GATK
updated 3.7 years ago by • 0 • written 6.3 years ago by ▴ 200
3
votes
5
replies
6.5k
views
add sample name to bam header based on bam file name
samtools
updated 3.9 years ago by 164k • written 3.9 years ago by ▴ 200
0
votes
0
replies
742
views
convert bam to cram with non-local reference fasta
samtools cram
3.9 years ago by Ana ▴ 200
0
votes
3
replies
8.5k
views
012 genotype matrix using vcf tools
vcftools genotype-matrix
updated 17 months ago by 44k • written 7.3 years ago by ▴ 200
1
vote
2
replies
1.5k
views
how to calculate the proportion of SNPs with DP more than 5
r depth of coverage
updated 5.0 years ago by 20 • written 7.2 years ago by ▴ 200
0
votes
0
replies
993
views
how to calculate genetic position for each marker from the genetic map file?
genetic-position map
updated 20 months ago by 44k • written 5.6 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 5.7 years ago by 36k • written 5.7 years ago by ▴ 200
3
votes
1
reply
1.8k
views
Assign a genomic region to a window
R windows bioconductor GenomicRanges
updated 5.8 years ago by 4.0k • written 5.8 years ago by ▴ 200
0
votes
2
replies
4.0k
views
How to add significance level to correlation heatmap using ggplot2
ggplot correlation r
updated 5.8 years ago by 36k • written 5.8 years ago by ▴ 200
2
votes
7
replies
4.0k
views
extract sample DP values from VCF
vcf perl vcftools
updated 17 months ago by 44k • written 7.7 years ago by ▴ 200
3
votes
1
reply
3.6k
views
difference between read depth (DP) at site (INFO) and sample(FORMAT) level
read depth vcf
updated 6.0 years ago by 12k • written 7.7 years ago by ▴ 200
4
votes
6
replies
1.6k
views
Attaching genotypes in the vcf files to individual ID
genotype
updated 6.0 years ago by 12k • written 6.6 years ago by ▴ 200
3
votes
1
reply
8.6k
views
genomic inflation factor and how to use it to estimate adjusted P-values in GWAS?
GWAS lambda
updated 6.1 years ago by ★ 3.0k • written 6.1 years ago by ▴ 200
0
votes
1
reply
2.3k
views
SNPs in high LD after LD pruning
LD SNPrelate
updated 6.2 years ago by 88k • written 6.2 years ago by ▴ 200
1
vote
2
replies
1.5k
views
tools to align DNA sequences against protein sequence
fastq alignment DNA
updated 20 months ago by 44k • written 6.4 years ago by ▴ 200
1
vote
0
replies
1.5k
views
hypergeometric test on outlier SNPs
outliers hypergeometric test R
6.4 years ago by Ana ▴ 200
1
vote
1
reply
1.3k
views
TukeyHSD does not match the box plot
depth of coverage anova
6.4 years ago by Ana ▴ 200
1
vote
18
replies
4.7k
views
Compute correlation for depth of coverage between 2 datasets with different length in R
depth of coverage correlation R
updated 6.6 years ago by 12k • written 6.6 years ago by ▴ 200
12
votes
29
replies
6.5k
views
compute depth of coverage for certain regions of the genome using samtools depth
depth of coverage samtools
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 200
2
votes
5
replies
2.6k
views
no output after running samtools depth
samtools bam
6.6 years ago by Ana ▴ 200
4
votes
4
replies
1.9k
views
downloading 1000 genomes project bam files in the background
bam
6.6 years ago by Ana ▴ 200
4
votes
8
replies
4.7k
views
downloading bam files of phase 3 of 1000 genomes project
1000genomes bam
updated 20 months ago by 44k • written 6.6 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
6.7 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 6.9 years ago by 35k • written 6.9 years ago by ▴ 200
4
votes
5
replies
2.0k
views
multiple DNA reads aligned to the same gene
alignment protein whole genome
6.9 years ago by Ana ▴ 200
1
vote
7
replies
1.8k
views
finding function of genes from their coordinates
gene annotation
6.9 years ago by Ana ▴ 200
1
vote
1
reply
1.3k
views
LD between CNVs and exterior SNPs
SNP cnv ld
6.9 years ago by Ana ▴ 200
2
votes
1
reply
2.5k
views
how to adjust a Manhattan plot for bayes factor
manhattan plot bayes factor
updated 7.1 years ago by 20 • written 7.1 years ago by ▴ 200
0
votes
3
replies
2.5k
views
error with running distruct.py in fastSTRUCTURE
fastSTRUCTURE admixture proportions
updated 7.1 years ago by 20 • written 7.3 years ago by ▴ 200
1
vote
3
replies
4.5k
views
determining appropriate window size for identifying highly differentiated SNPs
window-size genome-scan
updated 7.2 years ago by 88k • written 7.2 years ago by ▴ 200
4
votes
7
replies
2.5k
views
convert population allele count data into population allele frequency
allele frequency alle count python
updated 7.2 years ago by 88k • written 7.2 years ago by ▴ 200
0
votes
4
replies
1.9k
views
how to extract DP for individuals from the same population and save them in a file
vcf-file depth of coverage
updated 7.2 years ago by 164k • written 7.2 years ago by ▴ 200
4
votes
6
replies
1.6k
views
conditional replacing rows with 9
bash text-processing
updated 7.2 years ago by ★ 2.7k • written 7.2 years ago by ▴ 200
4
votes
8
replies
5.4k
views
012 genotype matrix using vcf tools (converting rows to columns)
genotype-matrix vcftools
updated 21 months ago by 44k • written 7.3 years ago by ▴ 200
1
vote
2
replies
2.5k
views
how to print a specific column condition in multiple files
Unix text-processing
updated 7.2 years ago by 88k • written 7.2 years ago by ▴ 200
1
vote
1
reply
2.8k
views
smartpca error running
software error SNP smartpca eigensoft
7.3 years ago by Ana ▴ 200
4
votes
6
replies
4.3k
views
how to run STRUCTURE command n times for each K value?
STRUCTURE bash
updated 7.4 years ago by 12k • written 7.4 years ago by ▴ 200
2
votes
7
replies
5.1k
views
running a perl script multiple times; input and output files are required
perl parallelization
updated 7.4 years ago by 164k • written 7.4 years ago by ▴ 200
5
votes
2
replies
1.4k
views
extract groups of SnPs and store them in separate files
SNP subsetting
7.4 years ago by Ana ▴ 200
5
votes
5
replies
1.9k
views
how can I keep only those SNP in file "a" which match to SNPs in file "b"?
row genotype file
updated 7.4 years ago by 47k • written 7.4 years ago by ▴ 200
23
votes
19
replies
3.5k
views
restructure rows and columns in perl or python (Interleaving columns by row pairs)
perl rows columns dataframe python
updated 7.5 years ago by 47k • written 7.5 years ago by ▴ 200
3
votes
12
replies
3.5k
views
how to extract a random set of SNP from a SNP table
SNP random sample extraction
updated 7.6 years ago by 36k • written 7.6 years ago by ▴ 200
0
votes
2
replies
2.3k
views
extract DP of heterozygotes from vcf file
vcffile heterozygotes sample read depth
updated 7.6 years ago by 164k • written 7.6 years ago by ▴ 200
3
votes
4
replies
9.4k
views
how to filter vcf file based on sample DP? vcf tools does not work
vcf-filtering sample DP
7.7 years ago by Ana ▴ 200
0
votes
2
replies
3.2k
views
calculating genotype quality from genotype likelihood
FreeBayes genotype likelihood genotype quality
updated 7.7 years ago by ▴ 70 • written 7.7 years ago by ▴ 200
2
votes
3
replies
1.8k
views
creating for loops in R for nGS data
R loops
updated 7.8 years ago by ★ 4.7k • written 7.8 years ago by ▴ 200
47 results • Page 1 of 1
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