vplagnol ExomeDepth issues

vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.

59 stars 26 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

High Number of Deletion Calls and Correlation Discrepancy in ExomeDepth Analysis

#61 valeandri opened 7 months ago
0
Genotyping Variant Calls

#60 justin-greenblatt opened 8 months ago
0
Creating a Baseline for calling CNV's for XX and XY samples

#59 justin-greenblatt opened 8 months ago
0
Confusion about expected number of CNV calls

#58 tsin-lau opened 9 months ago
0
Documentation

#57 pd3 closed 10 months ago
4
Error in countBamInGRanges

#56 Avinash-git-py opened 11 months ago
0
Nothing returns for CNV.calls

#55 lidd77 opened 1 year ago
2
A possible bug: getBamCounts returns 0 for every exon region

#54 lidd77 opened 1 year ago
0
how to calculate the absoulte copy number by this tool?

#53 lidd77 opened 1 year ago
1
Error in creating vignette

#52 skgs1970 opened 1 year ago
4
install Error

#51 user-tq closed 1 year ago
4
ExomeDepth installation fail

#50 Leelouh opened 1 year ago
4
How to get the Correlation between the test and selected reference after running CallCNV function

#49 AshwinKoppayi closed 1 year ago
2
Problem loading bed file in ExomeDepth. How to load bed file in ExomeDepth using Rstudio.

#48 SoumyadipGhosh98 closed 1 year ago
0
Facing some troubles while running ExomeDepth

#47 frasca17 opened 2 years ago
0
exomedepth in R 4.1.2

#46 AntonisSaphetor opened 2 years ago
0
unable to find an inherited method for function ‘scanFa’ for signature ‘"logical", "GRanges"’

#45 xiucz opened 2 years ago
0
Error in `[<-.data.frame`(`*tmp*`, , column.name, value = c(NA_character_, : replacement has 2 rows, data has 0

#44 worker000000 opened 2 years ago
1
error in CallCNVs function

#43 lmanchon opened 3 years ago
8
Target or bait, which BED file should I use?

#42 ghost opened 3 years ago
0
Chromosome, start and end vector must have the same lengths

#41 zgtman closed 9 months ago
7
Negative BF value

#40 zgtman opened 3 years ago
0
error in getBamCounts:[samopen] no @SQ lines in the header

#39 jeetendra-kuld opened 3 years ago
0
Error in using getBamCounts

#38 Martaprf opened 3 years ago
1
Confusing warnings using getBamCounts (ExomeDepth v.1.1.15)

#37 PaolaD opened 3 years ago
2
VCF output

#36 fgvieira opened 3 years ago
9
R crashes with very specific input

#35 kendrickkoo opened 3 years ago
5
Bayes Factor for all targets, not only the cnv calls

#34 vinzenzmay closed 3 years ago
1
Having more than 1 control after similarity search

#33 Fred-07 opened 3 years ago
1
reads ratios for regions not called as CNVs

#32 rajitz opened 4 years ago
0
Support for GRCh38?

#31 MikeHala opened 4 years ago
3
Error in getBamCounts when adding a reference Fasta

#30 ftucos closed 4 years ago
3
default min.mapq

#29 josianne-bioinf closed 4 years ago
0
Vignette and documentation for bin.length of select.reference.set are inconsistent

#28 bpow opened 4 years ago
1
correlation threshold

#27 rajitz closed 4 years ago
2
Error in Exomedepth CallCNVs function

#26 Shrutik08 closed 4 years ago
2
documentation does not reflect latest 1.1.15 changes

#25 jamigo opened 4 years ago
3
Parallelization possible?

#24 ghost opened 4 years ago
0
Genotyping within trios

#23 vinzenzmay opened 4 years ago
1
Error at the end of getBam Counts and output is not S4.

#22 nelsonchanhk closed 4 years ago
14
Different type of CNV with same start coordinate

#21 huzitu opened 4 years ago
0
RangeData objects are deprecated

#20 SouzaBB closed 4 years ago
12
Deletions with more reads than expected

#19 haraldgrove opened 5 years ago
4
the test samples has only 2 bins with more than 5 reads

#18 frankMusacchia opened 5 years ago
2
Counts from CRAM files

#17 ghost opened 5 years ago
12
segfault "memory not mapped" during getBamCounts

#16 wiraki opened 5 years ago
0
plot_CNV with exon names error

#15 przemekl closed 6 years ago
1
Fasta files

#14 laranonell closed 6 years ago
7
Fixed description of include.chr option

#13 wiraki closed 6 years ago
1
For using it on Rstudio windows

#12 amrita1983 opened 6 years ago
4