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questions
0
votes
2
replies
874
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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
4 months ago by
pragnapcu
• 0
0
votes
1
reply
381
views
How do I integrate GRCh38 CADD v1.6 offline with ANNOVAR?
CADD
v1.6
ANNOVAR
updated 5 months ago by
barslmn
★ 1.8k • written 5 months ago by
pragnapcu
• 0
2
votes
5
replies
503
views
How Haplotypecaller could call a 17-bp duplication that is not seen in sorted bam (in IGV)?
BaseRecalibrator
IGV
GATK
HaplotypeCaller
frameshiftinsertion
11 months ago by
pragnapcu
• 0
0
votes
4
replies
496
views
Why do I see sudden rise in TOTAL COUNT of my bam. I dont think it is duplication?
BAM
IGV
GATK
duplication
11 months ago by
pragnapcu
• 0
2
votes
2
replies
479
views
How to Visualize unmapped bam generated from GATK FastqToSam?
FastqToSam
UnmappedBam
GATK
11 months ago by
pragnapcu
• 0
0
votes
0
replies
440
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
11 months ago by
pragnapcu
• 0
2
votes
3
replies
828
views
Why different read depth on IGV and in VCF for a variant
depth
GATK
read
haplotypecaller
IGV
updated 13 months ago by
Friederike
8.8k • written 13 months ago by
pragnapcu
• 0
0
votes
1
reply
402
views
How can I identify common variants in siblings with same disorder after joint calling?
joint
calling
variants
common
Shared
updated 13 months ago by
Pierre Lindenbaum
157k • written 13 months ago by
pragnapcu
• 0
0
votes
0
replies
296
views
How do I get single multianno.txt file for multiple samples from Annovar?
joint
table_annovar.pl
GATK
Annovar
typing
13 months ago by
pragnapcu
• 0
0
votes
1
reply
535
views
How to select dataset from 1000 genome
1000genomes
vcf
updated 6 months ago by
Ram
40k • written 2.1 years ago by
pragnapcu
• 0
3
votes
5
replies
1.1k
views
Where do I get a WES dataset of size <1GB
WGS
WES
genomics
updated 2.1 years ago by
German.M.Demidov
★ 2.9k • written 2.1 years ago by
pragnapcu
• 0
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