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questions
0
votes
0
replies
145
views
Requesting Insights on Potential Complex Structural Event Indicated by IGV
Manta
IGV
variant
translocation
structural
14 days ago by
pragnapcu
• 0
0
votes
2
replies
282
views
Error Reading gencode.v38.genes.json.gz File in SvAnna CLI Tool
Structural-Variant
SVAnna
7 weeks ago by
pragnapcu
• 0
0
votes
2
replies
1.1k
views
Why the number of reads in bam generated by GATK haplotype caller are more than the bam generated after GATK baserecalibrator
BaseRecalibrator
BAM
GATK
READ
HaplotypeCaller
11 months ago by
pragnapcu
• 0
0
votes
1
reply
651
views
How do I integrate GRCh38 CADD v1.6 offline with ANNOVAR?
CADD
v1.6
ANNOVAR
updated 12 months ago by
barslmn
★ 2.1k • written 12 months ago by
pragnapcu
• 0
2
votes
5
replies
692
views
How Haplotypecaller could call a 17-bp duplication that is not seen in sorted bam (in IGV)?
BaseRecalibrator
IGV
GATK
HaplotypeCaller
frameshiftinsertion
18 months ago by
pragnapcu
• 0
0
votes
4
replies
662
views
Why do I see sudden rise in TOTAL COUNT of my bam. I dont think it is duplication?
BAM
IGV
GATK
duplication
18 months ago by
pragnapcu
• 0
2
votes
2
replies
614
views
How to Visualize unmapped bam generated from GATK FastqToSam?
FastqToSam
UnmappedBam
GATK
18 months ago by
pragnapcu
• 0
0
votes
0
replies
524
views
How can I give dbscsv11.txt.gz and dbscsv11.txt.gz.tbi to tableannovar --protocol instead of dbscsv11.txt and dbscsv11.txt.tbi?
dbscsnv
GATK
Annovar
18 months ago by
pragnapcu
• 0
3
votes
3
replies
1.1k
views
Why different read depth on IGV and in VCF for a variant
depth
GATK
read
haplotypecaller
IGV
updated 20 months ago by
Friederike
8.9k • written 20 months ago by
pragnapcu
• 0
0
votes
1
reply
514
views
How can I identify common variants in siblings with same disorder after joint calling?
joint
calling
variants
common
Shared
updated 20 months ago by
Pierre Lindenbaum
161k • written 20 months ago by
pragnapcu
• 0
0
votes
0
replies
455
views
How do I get single multianno.txt file for multiple samples from Annovar?
joint
table_annovar.pl
GATK
Annovar
typing
20 months ago by
pragnapcu
• 0
0
votes
1
reply
642
views
How to select dataset from 1000 genome
1000genomes
vcf
updated 13 months ago by
Ram
43k • written 2.7 years ago by
pragnapcu
• 0
3
votes
5
replies
1.3k
views
Where do I get a WES dataset of size <1GB
WGS
WES
genomics
updated 2.7 years ago by
German.M.Demidov
★ 2.9k • written 2.7 years ago by
pragnapcu
• 0
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