issues
search
lima1
/
PureCN
Copy number calling and variant classification using targeted short read sequencing
https://bioconductor.org/packages/devel/bioc/html/PureCN.html
Artistic License 2.0
127
stars
32
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Issue 320
#326
lima1
closed
1 year ago
0
Updated documentation and comments: --max-allele-counts, dbSNP member…
#325
ddrichel
closed
10 months ago
1
How to set up sex of PON
#324
lmanchon
closed
11 months ago
17
PureCN with ultra-deep sequenced plasma gene-panels
#323
RomainBosselut
closed
11 months ago
1
'long flag "seg-file" is invalid'
#322
h170607
closed
1 year ago
9
Effect of --max-copy-number parameter on purity/ploidy and copy number estimates
#321
ddrichel
closed
10 months ago
4
Mutect2 drops MBQ to 20 in overlapped reads
#320
sleyn
opened
1 year ago
4
Encountering error while running preprocessIntervals function
#319
gagank4911
closed
6 months ago
4
pureCN output genes.csv vs loh.csv
#318
hfl112
closed
1 year ago
1
NOISY SEGMENTATION in most samples
#317
WangKang-Leo
closed
1 year ago
4
PureCN segmentation and VCF do not overlap
#316
pavamateo
opened
1 year ago
1
Error creating NormalDB from GATK CreateSomaticPanelOfNormals output
#315
Moe94
closed
1 year ago
6
Error in the first step of PureCN
#314
fi1d18
closed
10 months ago
1
poor GOF in most samples
#313
atimms
closed
1 year ago
7
Question regarding the vcf output
#312
mkyriak
closed
1 year ago
4
Question regarding version 2.4 PureCN
#311
maxanes
closed
1 year ago
10
Question about solutions interpretation and PON
#310
tettamanzif
closed
12 months ago
11
Question: testing additional SNPS
#309
akaviaLab
closed
1 year ago
1
Question: Using other variant callers?
#308
akaviaLab
closed
1 year ago
2
Potential VCF issue - char '/' not in lookup table
#307
emmabailey94
closed
1 year ago
2
How to extract BAF from PureCN output files, which file to use ?
#306
lmanchon
closed
1 year ago
3
Ignore DB flag if it only contains NAs (#301).
#305
lima1
closed
1 year ago
0
Fix wrongly formatted error message (#302).
#304
lima1
closed
1 year ago
0
Error in PureCN Integration with Nextflow: misalignment between tumor coverage file and normalDB
#303
aldosr
closed
1 year ago
3
mpileup vcf error DB info field
#302
kristianunger
closed
1 year ago
3
Inconsistent VCF File Validation Request for Utilizing pureCN with MuTect
#301
DimitrisGrig
closed
1 year ago
1
Dimension of Tangent Normal Projection
#300
artuuge
closed
1 year ago
3
Attempt in fixing #298.
#299
lima1
closed
1 year ago
0
Strange notation in _genes.csv
#298
Jongseong-Ahn
closed
1 year ago
4
Potential simple fix for #260.
#297
lima1
closed
1 year ago
0
Update GenomicsDB functions for new API
#296
lima1
closed
1 year ago
0
Attempt in fixing #292.
#295
lima1
closed
1 year ago
0
Potential input for phylogenic analyses
#294
WangKang-Leo
closed
1 year ago
4
Question - command to use with GATK panel of normals
#293
akaviaLab
closed
1 year ago
1
callAlterations always outputs first solution
#292
un-saku
closed
1 year ago
1
Error in segmentByPairedPSCBS.default: All genotypes ('muN') are NAs
#291
leap-ahead225
closed
1 year ago
2
The distribution of purity
#290
WangKang-Leo
closed
1 year ago
6
Prepare 2.6.1
#289
lima1
closed
1 year ago
0
Instability purity/ploidy output with same seed
#288
waemm
closed
1 year ago
1
error/warning with NormalDB.R
#287
bosmont
closed
1 year ago
7
Subsampling SNP data
#286
waemm
closed
1 year ago
2
Fixed wrong return codes (#284)
#285
lima1
closed
1 year ago
0
NormalDB.R exits with status 1 when it run for CNVkit
#284
sleyn
closed
1 year ago
2
Added support for specifying RDS version (#255).
#283
lima1
closed
1 year ago
0
Issue 258
#282
lima1
closed
1 year ago
0
Fixed a crash when input VCF contains NAs in BQ (#249).
#281
lima1
closed
1 year ago
0
Filter homozygous germline variants when calculating MAFs (#254).
#280
lima1
closed
1 year ago
0
Error running PureCN.R
#279
bosmont
closed
1 year ago
3
different result when using same sample but with diff reference (of hg19 and hg38)
#278
nameOnStone
closed
1 year ago
5
Snp panel design
#277
waemm
closed
1 year ago
4
Previous
Next