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brentp
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duphold
don't get DUP'ed or DEL'ed by your putative SVs.
MIT License
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DHGT Missing for Manta DEL/DUP and Delly DEL
#54
MikeWLloyd
closed
7 months ago
3
Cutoff for duplications
#53
robertzeibich
opened
1 year ago
6
Should the tool duphold also work on small deletions <50bp?
#52
robertzeibich
opened
1 year ago
4
svtype = variant.info.get("SVTYPE", "SV")
#51
Jokendo-collab
opened
1 year ago
2
IndexDefect error in Version 0.2.1 - call for update in bioconda
#50
sunjh22
opened
1 year ago
1
Not every line was annotated?
#49
xiucz
opened
1 year ago
2
using duphold on a multisample trio VCF file
#48
prasundutta87
opened
2 years ago
2
The "REF prefixes differ" followed by Failed to merge alleles
#47
jjfarrell
opened
2 years ago
2
missing insertion
#46
Danisov
opened
2 years ago
4
Duphold with Nanopore data?
#45
AnneBoshove
opened
2 years ago
9
setting DUPHOLD_SAMPLE_NAME doesn't work
#44
am8265
opened
2 years ago
2
How to install duphold
#43
assane-mbodj
closed
3 years ago
11
Feature Request: Duphold Stats for Insertions
#42
jjfarrell
opened
3 years ago
2
duphold use with gVCF files
#41
am8265
opened
3 years ago
4
IndexError from Smoove calls
#40
cagaser
opened
3 years ago
8
duphold and clever: wrong annotation?
#39
cagaser
closed
3 years ago
2
duphold for MantaDUP(SVTYPE=DUP) are missing, INS are present
#38
am8265
closed
3 years ago
14
DHSP for duplications?
#37
natalia-linhares
opened
3 years ago
1
IndexError with Svaba caller vcf
#36
AhmedArslan
closed
4 years ago
2
How the coverage is estimated
#35
kasiatom
closed
4 years ago
2
Couldn't find sample from bam or ENV in vcf
#34
moldach
closed
4 years ago
6
SV Size and duphold
#33
jjfarrell
closed
4 years ago
2
Fix typo in the GCF INFO field.
#32
cbrueffer
closed
4 years ago
1
calling copy number based on duphold values
#31
lee039
opened
4 years ago
2
Error running Duphold, "expected AD field in snps VCF"
#30
johnemajor
opened
4 years ago
12
Fix out of bounds error.
#29
roryk
closed
4 years ago
1
Range error in version 0.2
#28
naumenko-sa
closed
4 years ago
0
Wrong tag
#27
dpryan79
closed
4 years ago
3
Problem Annotating Manta Tandem Duplications
#26
apaul7
closed
5 years ago
5
No error generated but duphold output missing last few lines.
#25
jjfarrell
opened
5 years ago
18
version controlled docker image?
#24
apaul7
closed
5 years ago
2
SIGSEGV: Illegal storage access. (Attempt to read from nil?)
#23
lindenb
closed
5 years ago
6
"expected GQ field in snps VCF" while (I think !) my vcf contains FORMAT/GQ
#22
lindenb
closed
5 years ago
6
error: "couldn't find sample from bam:or ENV in vcf"
#21
raungar
closed
5 years ago
7
Non transmission
#20
brentp
closed
5 years ago
0
--Sample name function can be useful
#19
idraktt
closed
5 years ago
3
Paper
#18
brentp
closed
5 years ago
0
what size flanking region is used to calculate DHFFC?
#17
JoWhi
closed
5 years ago
11
SNP annotation filters
#16
dmckean
closed
5 years ago
2
Exit without any useful information
#15
biozzq
closed
5 years ago
8
Can I set the parameter --snp as null?
#14
biozzq
closed
5 years ago
1
How is DHSP computed?
#13
raul-w
opened
5 years ago
2
v0.1.0: Error while calculating read depth of variants located beyond the first chromosome
#12
raul-w
closed
5 years ago
4
Logging information ended up in output file
#11
wdecoster
closed
5 years ago
3
Ignoring bases with 0 coverage while calculating read depth
#10
raul-w
closed
5 years ago
4
How does duphold treat N tracts
#9
dminkley
closed
5 years ago
5
support for long reads
#8
brentp
closed
5 years ago
0
Snp indel
#7
brentp
closed
5 years ago
0
Dev
#6
brentp
closed
5 years ago
0
local fold-change
#5
brentp
closed
5 years ago
1
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