brentp duphold issues - Githubissues

brentp / duphold

don't get DUP'ed or DEL'ed by your putative SVs.

MIT License

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issues

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DHGT Missing for Manta DEL/DUP and Delly DEL

#54 MikeWLloyd closed 9 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 2 years ago
1
Not every line was annotated?

#49 xiucz opened 2 years 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 3 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 4 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 5 years ago
1
Range error in version 0.2

#28 naumenko-sa closed 5 years ago
0
Wrong tag

#27 dpryan79 closed 5 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 6 years ago
2
v0.1.0: Error while calculating read depth of variants located beyond the first chromosome

#12 raul-w closed 6 years ago
4
Logging information ended up in output file

#11 wdecoster closed 6 years ago
3
Ignoring bases with 0 coverage while calculating read depth

#10 raul-w closed 6 years ago
4
How does duphold treat N tracts

#9 dminkley closed 6 years ago
5
support for long reads

#8 brentp closed 6 years ago
0
Snp indel

#7 brentp closed 6 years ago
0
Dev

#6 brentp closed 6 years ago
0
local fold-change

#5 brentp closed 6 years ago
1