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questions
0
votes
0
replies
400
views
Why does bcftools call from different max-depth (-d) value in mpileup give inconstant GT values?
vcf
variant-calling
bcftools
mpileup
updated 11 months ago by
Ram
43k • written 15 months ago by
magnolia
▴ 20
0
votes
0
replies
321
views
Which files contain overview information from Monarch Initiative?
monarch
initiative
16 months ago by
magnolia
▴ 20
1
vote
2
replies
687
views
How to obtain upstream variant genes?
snp
dbsnp
gene
variant
17 months ago by
magnolia
▴ 20
4
votes
8
replies
1.2k
views
Is possible to run VEP without consequence calculation?
vep
annotation
19 months ago by
magnolia
▴ 20
1
vote
2
replies
483
views
Is there a resource on how to create variant annotator from scratch?
annotation
variant
19 months ago by
magnolia
▴ 20
0
votes
0
replies
392
views
How assign PAR regions to X or Y for an rsID in VCF?
vcf
rsid
par
20 months ago by
magnolia
▴ 20
5
votes
10
replies
2.2k
views
How to change chromosome names in assembly fasta downloaded from NCBI?
grch38
ncbi
grch37
fasta
20 months ago by
magnolia
▴ 20
0
votes
0
replies
561
views
How to install/run pysam bcftools plugins?
bcftools
pysam
updated 11 months ago by
Ram
43k • written 20 months ago by
magnolia
▴ 20
1
vote
2
replies
505
views
How variant locations work when there is an INDEL around?
snp
indel
variant
21 months ago by
magnolia
▴ 20
1
vote
4
replies
938
views
How to insert dbSNP in a database?
dbsnp
database
21 months ago by
magnolia
▴ 20
9
votes
18
replies
3.2k
views
How to determine assembly of a VCF?
vcf
updated 21 months ago by
LauferVA
4.2k • written 22 months ago by
magnolia
▴ 20
5
votes
4
replies
3.1k
views
Is there equivalent of bgzip in Python?
python
bgzip
2.1 years ago by
magnolia
▴ 20
3
votes
8
replies
1.9k
views
Why VCF POS different in dbSNP and ClinVar?
vep
clinvar
dbsnp
vcf
2.4 years ago by
magnolia
▴ 20
0
votes
2
replies
731
views
How to parse VCF in Node/Javascript? (equivalent of pyVCF)
javascript
node
vcf
2.4 years ago by
magnolia
▴ 20
5
votes
5
replies
1.6k
views
Why VEP doesn't take strand into account?
vep
ensembl
snp
updated 3.3 years ago by
Emily
23k • written 3.3 years ago by
magnolia
▴ 20
3
votes
7
replies
1.2k
views
Why VEP annotates non-variants (homozygous reference)?
vep
ensembl
SNP
updated 3.3 years ago by
Emily
23k • written 3.3 years ago by
magnolia
▴ 20
1
vote
1
reply
901
views
How to get human gene locations via Python?
gene
python
3.8 years ago by
magnolia
▴ 20
6
votes
5
replies
2.1k
views
VEP outputs the similar INFO CSQ data multiple times
VEP
VCF
TSV
ensembl
annotation
updated 20 months ago by
Kermit
▴ 90 • written 4.0 years ago by
magnolia
▴ 20
0
votes
7
replies
1.5k
views
What's the best way to serve VCF data on web?
vcf
web
database
postgres
updated 4.1 years ago by
d-cameron
★ 2.9k • written 4.1 years ago by
magnolia
▴ 20
0
votes
9
replies
1.4k
views
Adding consequences field (INFO) when using --allow_non_variant in VEP
vep
vcf
annotation
updated 4.3 years ago by
Emily
23k • written 4.3 years ago by
magnolia
▴ 20
0
votes
2
replies
920
views
Is there any inheritance information source other than OMIM and free for commercial use?
gene
database
variant
recessive
dominant
5.0 years ago by
magnolia
▴ 20
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