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cancerit
/
alleleCount
Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
http://cancerit.github.io/alleleCount/
GNU Affero General Public License v3.0
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Choosing SNPs
#78
bounlu
opened
3 months ago
3
Is LWP::UserAgent required?
#77
ItIsI-Orient
closed
1 year ago
1
.exe file
#76
vlachosg37
closed
1 year ago
1
Scipt convertAlleleCounts.r deleted?
#75
justalilibit
closed
1 year ago
1
how to install in R
#74
esraajamal
opened
1 year ago
1
Can I use this tools on RNAseq BAM file ?
#73
panxiaoguang
closed
2 years ago
2
Unpaired data - No alleleCount when reads available
#72
ShixiangWang
closed
6 months ago
9
Confusing error when input is unmapped
#71
keiranmraine
opened
2 years ago
0
Feature/convert to json
#70
davidrajones
closed
3 years ago
0
Null Iterator Error
#69
nitishnih
opened
3 years ago
6
base image update to Ubuntu 20.04
#68
keiranmraine
closed
3 years ago
0
htslib for dockerfile is not updated
#67
keiranmraine
closed
3 years ago
2
Error in cli help
#66
keiranmraine
opened
4 years ago
0
10X test data doesn't work
#65
keiranmraine
opened
4 years ago
0
AlleleCounter bahavior with soft-clipped reads
#64
DominikGlodzik
opened
4 years ago
1
Is htslib 1.10.2 supported?
#63
roryk
closed
3 years ago
1
"-b|--hts-file" isn't obvious means BAM/CRAM
#62
keiranmraine
opened
4 years ago
0
Running aC on scRNA BAMs (10X or otherwise)
#61
nansari-pour
closed
4 years ago
4
Integrate read end clipping in to allelecounter
#60
danchubb
opened
4 years ago
0
Clipping reads and reference bias
#59
danchubb
opened
4 years ago
3
sorting of loci file for dense-snps
#58
nurmians
opened
4 years ago
1
Feature/dokerization
#57
rulixxx
closed
5 years ago
0
Feature/dokerization
#56
rulixxx
closed
5 years ago
0
Feature/dokerization
#55
rulixxx
closed
5 years ago
0
Memory use vs. size of SNP list
#54
ilykos
opened
5 years ago
0
AlleleCounter for unpaired data
#53
m4merg
closed
5 years ago
1
Running alleleCounter with or without reference file
#52
ilykos
closed
5 years ago
1
WIP: Hotfix/v4.0.2 - DO NOT MERGE
#51
ghost
closed
5 years ago
2
Indel support
#50
ibwoo
closed
5 years ago
1
DO NOT MERGE! Hotfix/v4.0.1
#49
ghost
closed
5 years ago
3
Description
#48
nurmians
opened
6 years ago
3
10x data
#47
thelingxichen
closed
4 years ago
1
RNA STAR aligned files may have different flags
#46
ghost
opened
6 years ago
0
Feature/overlapping reads
#45
keiranmraine
closed
6 years ago
0
int(block_str) error
#44
girdhar3
closed
6 years ago
2
Add 10X processing mode.
#43
keiranmraine
closed
6 years ago
4
test failed: t/01bam.t .... Failed 235/235 subtests
#42
weiliuyuan
closed
6 years ago
3
allelecount runs endlessly or gets killed on CentOS 7
#41
mheskett
closed
6 years ago
3
Pre-release tag for fragment analysis
#40
keiranmraine
closed
6 years ago
0
Feature/wrap c
#39
keiranmraine
closed
6 years ago
0
Feature/wrap c
#38
keiranmraine
closed
6 years ago
1
C alleleCounter - filter by long form
#37
keiranmraine
closed
6 years ago
3
installation error
#36
mheskett
closed
6 years ago
8
installation error on linux
#35
mheskett
closed
6 years ago
0
Installation error
#34
keyuan
closed
6 years ago
2
Add 10X processing mode.
#33
constantAmateur
closed
6 years ago
1
Prototype overlapping read count corrections in alleleCounter.pl
#32
keiranmraine
closed
6 years ago
0
Feature/dense snp locations
#31
ghost
closed
7 years ago
0
migrate perl alleleCounter.pl to wrap the C version
#30
keiranmraine
closed
6 years ago
0
Option to run through file rather than use pileup/fetch
#29
ghost
closed
7 years ago
0
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