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2
votes
6
replies
809
views
What is the expected number of common/mutual/shared SNVs between two, three, four... unrelated individuals?
snv genomics variation snp human
10 weeks ago by Joel Wallenius ▴ 210
4
votes
8
replies
1.3k
views
Locating IBD candidates with just VCF files
Relatedness Genotypes IBD Haplotypes VCF
10 weeks ago by Joel Wallenius ▴ 210
0
votes
1
reply
463
views
GATK's CNV-caller output, genotype code?
GATK CNV NGS
updated 3 months ago by • 0 • written 20 months ago by ▴ 210
0
votes
6
replies
737
views
Parallel GWAS?
GWAS Parallel Chromosome
updated 10 months ago by 11k • written 10 months ago by ▴ 210
2
votes
4
replies
720
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping Variant-calling masking
updated 10 months ago by 142k • written 11 months ago by ▴ 210
0
votes
0
replies
381
views
What are the WES-specific settings when running GATK's variant recalibration step?
WES GATK recalibration exome
12 months ago by Joel Wallenius ▴ 210
0
votes
0
replies
335
views
A program that detects similar regions between samples in a multi-sample VCF file?
Relatedness IBD Haplotypes
18 months ago by Joel Wallenius ▴ 210
0
votes
0
replies
281
views
How many SNPs are needed to perform haplotype analysis on siblings and their mother?
haplotype linkage SNP pedigree
18 months ago by Joel Wallenius ▴ 210
2
votes
22
replies
2.3k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree linkage genetics
18 months ago by Joel Wallenius ▴ 210
5
votes
6
replies
1.1k
views
Can you not phase exome data?
phasing shapeit wes exome beagle
updated 20 months ago by 4.2k • written 20 months ago by ▴ 210
2
votes
2
replies
755
views
How to properly subset a bam file?
bam subset truncate
20 months ago by Joel Wallenius ▴ 210
6
votes
7
replies
1.9k
views
Convert a BAM from GRCh37 to hg19?
GRCh37 hg19 BAM
updated 21 months ago by 43k • written 22 months ago by ▴ 210
0
votes
0
replies
344
views
STR expansion detection on IonTorrent WES data?
repeat STR IonTorrent wes ngs short tandem
22 months ago by Joel Wallenius ▴ 210
0
votes
0
replies
366
views
"Best" freewares for linkage analyses?
Equilibrium Linkage Disequilibrum haplotyping
22 months ago by Joel Wallenius ▴ 210
4
votes
11
replies
1.4k
views
Bam file to Sanger-like chromatogram?
sanger visualization diagram plot bam
2.1 years ago by Joel Wallenius ▴ 210
3
votes
9
replies
1.2k
views
RC an entire bam file?
sam genome complement viewer alignment bam Reverse
2.1 years ago by Joel Wallenius ▴ 210
3
votes
10
replies
2.2k
views
Mate pairs and paired reads confusion
sequencing
2.1 years ago by Joel Wallenius ▴ 210
0
votes
0
replies
416
views
Alternatives to ExpansionHunter?
Repeat STR Expansion Genetics Repeats
2.2 years ago by Joel Wallenius ▴ 210
2
votes
4
replies
1.7k
views
GATK's GenomicsDBImport takes forever...
Variant GATK Calling
2.6 years ago by Joel Wallenius ▴ 210
0
votes
8
replies
1.3k
views
Best alignment software for mapping short DNA reads to transcriptome?
alignment Transcriptome DNA
4.3 years ago by Joel Wallenius ▴ 210
20
votes
26
replies
3.2k
views
Is there a command line tool that can take an alignment fasta and input and outputs an image?
alignment fasta image
updated 9 months ago by 21k • written 4.9 years ago by ▴ 210
0
votes
0
replies
765
views
AnnoVar with custom genomes?
AnnoVar Annovar
4.9 years ago by Joel Wallenius ▴ 210
0
votes
9
replies
5.4k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq rna-seq htseq FPKM TPM
updated 9 months ago by 82k • written 5.1 years ago by ▴ 210
2
votes
7
replies
1.4k
views
Where is the (hg19) reference data for transcript isoforms' relative abundances for each gene?
RNA-Seq transcriptomics isoforms
updated 5.0 years ago by 19k • written 5.0 years ago by ▴ 210
1
vote
19
replies
2.0k
views
Approximately following the GATK recommended workflow for DNA sequence data, my mpileup output files are empty
sequencing SNP genome next-gen
5.1 years ago by Joel Wallenius ▴ 210
2
votes
5
replies
1.5k
views
Given a list of RefSeq homo sapiens mRNA transcripts, what is the simplest way to get the corresponding sequences from some other related species?
alignment transcriptome orthology
6.1 years ago by Joel Wallenius ▴ 210
2
votes
1
reply
1.1k
views
Interpreting the output of an mRNA structural motif search algorithm
mRNA motif structure
updated 6.3 years ago by ★ 3.1k • written 6.3 years ago by ▴ 210
0
votes
2
replies
1.4k
views
Given a protein domain, like a TPR or zinc finger or some other one, can you predict what RNA sequence it binds to?
RNA RBP Protein Affinity
6.3 years ago by Joel Wallenius ▴ 210
0
votes
11
replies
3.1k
views
Getting MPI to work with MEME suite CPU parallelization in OpenSuse
meme mpi parallelization opensuse
updated 6.4 years ago by 35k • written 6.4 years ago by ▴ 210
0
votes
4
replies
1.3k
views
Find all nuclear genes the mRNA of which binds to the CLUH protein for transport to mitochondria?
mitochondria mRNA transport CLUH
updated 6.5 years ago by 22k • written 6.5 years ago by ▴ 210
0
votes
6
replies
3.5k
views
The meaning of '0' allele frequency in vcftools output
vcf vcftools MAF allele frequency allele
updated 6.6 years ago by 20 • written 6.6 years ago by ▴ 210
2
votes
8
replies
2.5k
views
Imposing a human reference genome onto a vcf file?
vcf genome sequencing SNP allele
updated 6.6 years ago by 161k • written 6.6 years ago by ▴ 210
32 results • Page 1 of 1
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