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Showing :
questions
2
votes
2
replies
3.6k
views
Python library for parsing bcftools stats file
bcftools
6.7 years ago by
William
★ 5.3k
0
votes
0
replies
3.9k
views
How to plot VCF missingness per sample (.imiss) and per variant (.lmiss) in python?
qc
plink
vcftools
vcf
updated 6.8 years ago by
Biostar
20 • written 7.2 years ago by
William
★ 5.3k
1
vote
1
reply
4.6k
views
Expression data missing in a GEO study
GEO
bioconductor
GEOquery
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
William
★ 5.3k
0
votes
2
replies
1.9k
views
Can IonProton sequencing data be processed using BWA + FreeBayes or CLC?
ionproton
6.9 years ago by
William
★ 5.3k
2
votes
2
replies
1.9k
views
Why do indel variants need a leading base according to the VCF spec?
vcf
updated 7.0 years ago by
Ram
43k • written 7.0 years ago by
William
★ 5.3k
7
votes
4
replies
3.7k
views
Recent comparison of BWA-mem versus Berkeley SNAP aligner, TP, TN and speed.
snap
bwa
updated 19 months ago by
Ram
43k • written 8.6 years ago by
William
★ 5.3k
35
votes
14
replies
44k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf
bcftools
updated 7 months ago by
ashotmarg2004
▴ 130 • written 7.8 years ago by
William
★ 5.3k
2
votes
1
reply
5.0k
views
CombineGVCFs + GenotypeGVCFs for Freebayes gVCF files?
freebayes
gvcf
7.2 years ago by
William
★ 5.3k
10
votes
7
replies
3.4k
views
Best visual and interactive genotype matrix (VCF) exploration tool
vcf
bcftools
interactive
visual
updated 7.2 years ago by
willgilks
▴ 360 • written 7.2 years ago by
William
★ 5.3k
3
votes
4
replies
2.9k
views
How to filter a VCF on a set of samples having genotypes containing the minor allele?
vcf
bcftools
snpsift
7.3 years ago by
William
★ 5.3k
45
votes
9
replies
15k
views
7 follow
Best Genome Browser To Look At Structural Variation Calls
updated 7.3 years ago by
graeme.grimes
▴ 10 • written 11.7 years ago by
William
★ 5.3k
3
votes
1
reply
2.9k
views
How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gff3 and VCF?
snpeff
updated 7.3 years ago by
Vitis
★ 2.5k • written 7.3 years ago by
William
★ 5.3k
2
votes
0
replies
2.3k
views
Recent comparison between variant effect prediction tools, mainly SnpEff v.s. Ensembl VEP
effect prediction
7.5 years ago by
William
★ 5.3k
1
vote
1
reply
2.3k
views
Merge phased SNP variants to haplotypes? And is vcfallelicprimitives reversible?
vcf
updated 7.5 years ago by
Biostar
20 • written 7.6 years ago by
William
★ 5.3k
2
votes
4
replies
4.2k
views
Cnvnator Genotype Regions Error : Can'T Find Bin 1000
updated 7.6 years ago by
cyrielle
▴ 10 • written 10.6 years ago by
William
★ 5.3k
0
votes
0
replies
2.0k
views
How does Plink (or any stats genetics tool) deal with missing genotypes in linear/logistic regression?
plink
linear regression
missing_genotypes
7.7 years ago by
William
★ 5.3k
11
votes
4
replies
2.6k
views
10 to 1000X speedup of BWA read alignment trough compressive mapping: MIT CORA
bwa
fastq
alignment
compression
updated 7.9 years ago by
Biostar
20 • written 8.0 years ago by
William
★ 5.3k
1
vote
3
replies
4.6k
views
Breakdancer Bam2Cfg.Pl , Coefficient Of Variation Is Too Large, Not Excluding Outliers?
breakdancer
updated 7.9 years ago by
Biostar
20 • written 10.7 years ago by
William
★ 5.3k
3
votes
3
replies
5.3k
views
How To Set Validation_Stringency In The Picard Api Directly From Java
picard
java
api
updated 8.1 years ago by
Biostar
20 • written 11.0 years ago by
William
★ 5.3k
6
votes
3
replies
2.9k
views
How To Use Unmapped Reads To Reconstruct Strains Specific Genome Segments?
denovo
solid
updated 8.1 years ago by
Philipp Bayer
8.4k • written 10.8 years ago by
William
★ 5.3k
5
votes
2
replies
1.7k
views
Is it good practice to convert lowest quality genotyes to missing?
vcf
qc
genotypes
updated 8.1 years ago by
Zev.Kronenberg
12k • written 8.1 years ago by
William
★ 5.3k
5
votes
8
replies
4.8k
views
Output per variant and per sample heterozygosity fraction from VCF.
vcf
qc
updated 2.7 years ago by
Pierre Lindenbaum
161k • written 8.1 years ago by
William
★ 5.3k
1
vote
1
reply
1.7k
views
Which Illumina data to generate for constructing benchmark SNP / SV genotypes
illumina
benchmarking
SNP
SV
8.1 years ago by
William
★ 5.3k
6
votes
6
replies
2.8k
views
How to plot a histogram for billions of genotype quality values?
vcf
quality
R
python
updated 8.1 years ago by
biocyberman
▴ 860 • written 8.1 years ago by
William
★ 5.3k
0
votes
5
replies
4.7k
views
How To Select A Private Snp With Gatk From A Multisample Vcf File
gatk
snp
updated 8.2 years ago by
Biostar
20 • written 11.3 years ago by
William
★ 5.3k
0
votes
0
replies
3.3k
views
Where to find gene annotation file for 1000 genomes phase 3 data / hs37d5/ b37 assembly .
gene
annotation
updated 20 months ago by
Ram
43k • written 8.4 years ago by
William
★ 5.3k
21
votes
5
replies
8.9k
views
Best Discordant Pair Structural Variant (Sv) Caller?
vcf
sv
discordant
variant
caller
updated 8.4 years ago by
Malachi Griffith
19k • written 10.8 years ago by
William
★ 5.3k
11
votes
3
replies
6.2k
views
Do freeBayes and platypus support gVCF (ie incremental variant calling for large sets of genomes)
platypus
gvcf
freebayes
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
William
★ 5.3k
5
votes
2
replies
3.7k
views
Library To Parse Absolute Reference Positions Of Indels From A Bam Cigar String
bam
sv
picard
api
updated 8.5 years ago by
Biostar
20 • written 10.7 years ago by
William
★ 5.3k
2
votes
2
replies
5.1k
views
How to annotate SNP variant records in a vcf file with IDs from a bed file?
vcf
bcftools
bed
updated 20 months ago by
Ram
43k • written 8.6 years ago by
William
★ 5.3k
2
votes
4
replies
3.6k
views
BCFTools view equivelent of GATK -T SelectVariants -sn sample_x --excludeNonVariants
bcftools
gatk
updated 20 months ago by
Ram
43k • written 8.6 years ago by
William
★ 5.3k
1
vote
1
reply
3.1k
views
how to add QualityOfDepth(QD) annotation to freebayes vcf
vcf
qualitybydepth
freebayes
updated 19 months ago by
Ram
43k • written 8.7 years ago by
William
★ 5.3k
3
votes
1
reply
6.8k
views
Best VCF file validator
vcf
updated 19 months ago by
Ram
43k • written 8.6 years ago by
William
★ 5.3k
0
votes
0
replies
3.0k
views
Installing mango genome browser: NoClassDefFoundError: org/eclipse/jetty/server/Handler
adam
mango
updated 16 months ago by
Ram
43k • written 8.9 years ago by
William
★ 5.3k
47
votes
9
replies
25k
views
Difference Between Somatic And Germline Variant Calling?
somatic
gatk
variant-calling
updated 9.0 years ago by
Biostar
20 • written 10.6 years ago by
William
★ 5.3k
0
votes
0
replies
2.4k
views
Tools for automatic or semi-automatic extraction of ontology concepts from GEO meta-data to RDF.
rdf
ontology
GEO
metadata
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
William
★ 5.3k
6
votes
2
replies
2.7k
views
Recent Review / Best practices for (meta) micro array expression data analysis
microarray
updated 23 months ago by
Ram
43k • written 9.4 years ago by
William
★ 5.3k
0
votes
0
replies
1.8k
views
I2B2( Informatics for Integrating Biology and the Bedside or alternatives) still used /developed?
clinical
updated 23 months ago by
Ram
43k • written 9.1 years ago by
William
★ 5.3k
4
votes
4
replies
3.8k
views
Official specs and API's for proteomics data (like Adam, VCF, HTS-JDK) (both file and distributed storage)
genomics
proteomics
api
specification
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
William
★ 5.3k
6
votes
3
replies
11k
views
Gatk Multi-Sample Vcf Variantfiltration
gatk
vcf
updated 9.3 years ago by
Biostar
20 • written 10.9 years ago by
William
★ 5.3k
3
votes
2
replies
2.7k
views
Looking for a bam file with aligned (error corrected) PacBio reads
bam
pacbio
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
William
★ 5.3k
4
votes
2
replies
7.1k
views
How To Convert A Multisample Vcf To A Format That Can Be Loaded In Haploview?
vcf
haploview
haplotype
ped
updated 2.3 years ago by
Ram
43k • written 10.5 years ago by
William
★ 5.3k
4
votes
2
replies
4.7k
views
Principal component analysis for proteomics data ( like SNPRelate )
pca
proteomics
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
William
★ 5.3k
2
votes
5
replies
4.3k
views
Which Snp Caller / Method To Use After Aligning Rna-Seq With Tophat
snp
tophat2
rna-seq
updated 10.2 years ago by
jockbanan
▴ 420 • written 11.0 years ago by
William
★ 5.3k
11
votes
9
replies
6.7k
views
6 follow
Standard Post Variant Call (Vcf) Analysis That Work Out Of The Box
vcf
analysis
updated 10.4 years ago by
alexej.knaus
▴ 130 • written 10.5 years ago by
William
★ 5.3k
0
votes
1
reply
2.7k
views
Split Contig Structural Variant Calling On Bac Contigs Aligned With Bwa-Mem.
sv
pindel
updated 10.5 years ago by
Biostar
20 • written 10.7 years ago by
William
★ 5.3k
10
votes
1
reply
6.9k
views
Vcftools Vcf-Stats Field Definitions
vcf
statistics
vcftools
updated 10.5 years ago by
dangenet
▴ 90 • written 10.5 years ago by
William
★ 5.3k
12
votes
5
replies
4.3k
views
Using Gatk On Inbred Species - What To Do With The Heterozygous Calls?
gatk
updated 10.6 years ago by
Ashutosh Pandey
12k • written 10.8 years ago by
William
★ 5.3k
2
votes
3
replies
2.5k
views
Do People Use Grid Computing For Ngs Analysis Or Just Local Cluster Computing (Sge/Pbs)
ngs
updated 10.6 years ago by
Spitshine
▴ 660 • written 10.6 years ago by
William
★ 5.3k
1
vote
3
replies
3.4k
views
Cnvnator Deletion Calls All Based On Mapping Quality Zero Reads?
cnv
quality
10.7 years ago by
William
★ 5.3k
139 results • Page
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