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0
votes
0
replies
183
views
VEP verisoning and GRCh37 vs GRCh38. conda/mamba/anaconda
ensembl
genomics
VEP
GRCh37
conda
8 weeks ago by
jon.klonowski
▴ 120
0
votes
0
replies
604
views
Comment:
Comment: Installing VEP in conda
8 weeks ago by
jon.klonowski
▴ 120
3
votes
5
replies
773
views
How to choose output when using a "By" function from a TxDb object; GenomicFeatures R
TxDb
GenomicFeatures
genomics
R
5 months ago by
jon.klonowski
▴ 120
2
votes
0
replies
773
views
Answer:
Answer: How to choose output when using a "By" function from a TxDb object; GenomicFeatu
5 months ago by
jon.klonowski
▴ 120
0
votes
1
reply
773
views
Comment:
Comment: How to choose output when using a "By" function from a TxDb object; GenomicFeatu
5 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
150
views
How to check for the most recent EnsDb Hsapiens verison?
genomics
ensembl
ensdb
ensembldb
5 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
337
views
Comment:
Comment: Command line VEP "Amino_acid" Output Column Inturperation: AA / AA * AA
5 months ago by
jon.klonowski
▴ 120
2
votes
3
replies
337
views
Command line VEP "Amino_acid" Output Column Inturperation: AA / AA * AA
VEP
ensembl
genetics
genomics
annotation
5 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
1.5k
views
Comment:
Comment: How do I split a genomicrange on chromosome and strand?
6 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
425
views
Comment:
Comment: how do you get an IN-FRAME deletion stop gain variant?
6 months ago by
jon.klonowski
▴ 120
1
vote
3
replies
425
views
how do you get an IN-FRAME deletion stop gain variant?
genomics
annotation
ensembl
VEP
genetics
6 months ago by
jon.klonowski
▴ 120
1
vote
1
reply
425
views
Answer:
Answer: how do you get an IN-FRAME deletion stop gain variant?
6 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
327
views
What is a good Standardized Beta/standardized regression coefficient in a genetics study?
regression
size
genomics
effect
genetics
beta
10 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
9.2k
views
Comment:
Comment: Pararellization in GATK 4
12 months ago by
jon.klonowski
▴ 120
0
votes
1
reply
561
views
gnomAD AF = 0 vs gnomAD AF = NA (gnomad V2)
annontation
rare
genomics
variant
gnomad
13 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
561
views
Answer:
Answer: gnomAD AF = 0 vs gnomAD AF = NA (gnomad V2)
13 months ago by
jon.klonowski
▴ 120
1
vote
0
replies
623
views
Answer:
Answer: Merged Reference Panel using WES data
13 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
694
views
Comment:
Comment: gnomAD reports variants with "NA" allele count and allele frequency
13 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
415
views
UCSC parameters for converting between human genome builds
genomics
bed
ucsc
genotyping
14 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
273
views
How important is aligning BAM files to the appropriate design file?
gatk
sequencing
genomics
wes
bam
15 months ago by
jon.klonowski
▴ 120
0
votes
1
reply
3.8k
views
Comment:
C: Version history and design files for exome kits from Agilent, Roche(Nimblegen),
16 months ago by
jon.klonowski
▴ 120
0
votes
1
reply
3.8k
views
Comment:
A: Version history and design files for exome kits from Agilent, Roche(Nimblegen),
16 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
274
views
Multiple Sequencing Platforms, One Interval File?
WES
sequencing
GATK
16 months ago by
jon.klonowski
▴ 120
1
vote
1
reply
585
views
Considerations when merging a gVCF with a VCF?
vcf
bcftools
gvcf
gatk
WES
updated 18 months ago by
kreenaijuriya
• 0 • written 18 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
818
views
Comment:
C: plink2: no file/directory libgfortran, search has found libgfortran
18 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
818
views
Comment:
C: plink2: no file/directory libgfortran, search has found libgfortran
18 months ago by
jon.klonowski
▴ 120
0
votes
4
replies
818
views
plink2: no file/directory libgfortran, search has found libgfortran
plink
genetics
vcf
sequencing
WES
updated 18 months ago by
Mensur Dlakic
★ 19k • written 18 months ago by
jon.klonowski
▴ 120
0
votes
1
reply
1.2k
views
Comment:
A: join vcf file with annotations file?
19 months ago by
jon.klonowski
▴ 120
0
votes
2
replies
410
views
Gene Location File - One Gene One Genomic Interval
genomics
genome
sequencing
SNP
burden
19 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
410
views
Answer:
A: Gene Location File - One Gene One Genomic Interval
19 months ago by
jon.klonowski
▴ 120
0
votes
0
replies
3.4k
views
Comment:
C: Downloadable File With Gene Locations
19 months ago by
jon.klonowski
▴ 120
0
votes
2
replies
2.0k
views
gatk SelectVariants odd behavior
gatk
selectvariants
vcf
filtering
SNP
updated 2.6 years ago by
cricgpu
• 0 • written 3.2 years ago by
jon.klonowski
▴ 120
8
votes
10
replies
2.3k
views
6 follow
Is Ingenuity Pathway Analysis still relevant for analyzing RNA-seq data?
IPA
RNA-Seq
NGS
dataanalysis
updated 3.0 years ago by
Morris_Chair
▴ 280 • written 3.0 years ago by
jon.klonowski
▴ 120
1
vote
1
reply
1.6k
views
Comment:
C: BCF Tools Filter on 1000Genomes Annotation
updated 3.2 years ago by
finswimmer
15k • written 3.2 years ago by
jon.klonowski
▴ 120
0
votes
1
reply
1.6k
views
Comment:
C: BCF Tools Filter on 1000Genomes Annotation
updated 3.2 years ago by
finswimmer
15k • written 3.2 years ago by
jon.klonowski
▴ 120
0
votes
0
replies
1.0k
views
Comment:
C: BCFTools Query: Avoid grouping Alt Alleles
3.2 years ago by
jon.klonowski
▴ 120
3
votes
5
replies
1.6k
views
BCF Tools Filter on 1000Genomes Annotation
bcftools
vcftools
annotation
filter
3.2 years ago by
jon.klonowski
▴ 120
2
votes
5
replies
5.7k
views
grep command on VCF
vcf
unix
grep
bcf
3.2 years ago by
jon.klonowski
▴ 120
1
vote
0
replies
5.7k
views
Answer:
A: grep command on VCF
3.2 years ago by
jon.klonowski
▴ 120
0
votes
0
replies
5.7k
views
Comment:
C: grep command on VCF
3.2 years ago by
jon.klonowski
▴ 120
0
votes
0
replies
1.6k
views
Comment:
C: BCF Tools Filter on 1000Genomes Annotation
3.2 years ago by
jon.klonowski
▴ 120
0
votes
0
replies
5.7k
views
Comment:
C: grep command on VCF
3.2 years ago by
jon.klonowski
▴ 120
0
votes
1
reply
1.0k
views
BCFTools Query: Avoid grouping Alt Alleles
bcftools
vcf
1000genomes
annotation
3.2 years ago by
jon.klonowski
▴ 120
0
votes
0
replies
3.1k
views
Comment:
C: PLINK vcf to binary files error: Unused command line option: --vcf
3.2 years ago by
jon.klonowski
▴ 120
0
votes
1
reply
3.1k
views
Comment:
C: PLINK vcf to binary files error: Unused command line option: --vcf
3.2 years ago by
jon.klonowski
▴ 120
0
votes
5
replies
3.1k
views
PLINK vcf to binary files error: Unused command line option: --vcf
plink
vcf
genomics
updated 3.2 years ago by
chrchang523
9.3k • written 3.2 years ago by
jon.klonowski
▴ 120
1
vote
0
replies
18k
views
Comment:
C: Sort VCF File by Position?
3.2 years ago by
jon.klonowski
▴ 120
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