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single-cell-genetics
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cellsnp-lite
Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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Incorrect output when using BD Rhapsody / STAR solo input
#79
sbamopoulos
closed
1 year ago
2
runtime and expected output
#78
ahoffrichter
opened
1 year ago
6
Question for minMAF parameter
#77
fe4960
closed
1 year ago
5
Automatically detect all chromosomes in bam
#76
chilampoon
opened
1 year ago
2
single cell RNA-seq cellsnp lite error mode 2b+ 1a
#75
drlaurenwasson
opened
1 year ago
1
Unable to install CellSNP-Lite from conda
#74
aseyedia
closed
1 year ago
1
Had any scripts to pick the distinctive SNP site from vireo file GT_donors.vireo.vcf.gz gene to distinguish multiple sample using PCR experiment
#73
honghh2018
opened
1 year ago
1
how can i build the preprocess vcf for mouse, like human common SNP vcf file, using GATK google warehouse snp data
#72
honghh2018
opened
1 year ago
1
ELBO plot decreasing instead of increasing to a plateau
#71
haigdjambazian
opened
1 year ago
2
Huge 10X scRNA-seq mouse data
#70
alexfernandes8a
opened
1 year ago
1
The mutation matrix input for SCITE
#69
alanfoleynibrt
closed
1 year ago
0
Filtering cells before or after cellsnp-lite
#68
haigdjambazian
closed
1 year ago
1
How to set -p (Slurm)
#67
flde
closed
1 year ago
1
AF for candidate SNP
#66
Zepeng-Mu
closed
1 year ago
2
Calling SNPs using multiple bam files with single cell data
#65
scachero
opened
2 years ago
5
minor updates
#46
hxj5
closed
2 years ago
0
Incorrect parameter passing causes segmentation fault
#45
adbeggs
opened
2 years ago
1
has pileup-ed in total 0 SNPs
#44
haigdjambazian
closed
2 years ago
7
Issue with reference for cellsnp-lite
#43
haigdjambazian
closed
2 years ago
2
Blank cellSNP.base.vcf
#42
alanfoleynibrt
closed
2 years ago
4
Incorporate indel?
#41
haochenz96
opened
2 years ago
3
Multi-threading not working for mtRNA genotying?
#40
teng-gao
closed
2 years ago
8
BAM filtering query - ok to have multiple primary alignments in BAM file?
#39
lucygarner
opened
2 years ago
7
Error message: Argument list too long
#38
Victor-fe
opened
2 years ago
1
verbose mode
#37
vjbaskar
closed
2 years ago
3
Empty o/p matrix files
#36
Parul-Kudtarkar
closed
2 years ago
2
empty output using cellsnp-lite with 10x and 1000 genome vcf file
#35
songeric1107
closed
2 years ago
8
[E::csp_pileup] could not parse name for chrom 20
#34
PietroD
closed
2 years ago
1
cellsnp-lite output not working with Vireo - reporting really high read depths
#33
dannyconrad
opened
2 years ago
1
Inflate operation failed
#32
AnjaliC4
opened
2 years ago
1
Handle SMART-Seq bams?
#31
teng-gao
closed
2 years ago
0
Region-level quantifications
#30
tohein
opened
2 years ago
1
update to v1.2.2
#29
hxj5
closed
2 years ago
0
definition of REF and ALT in mode 2
#28
bobermayer
closed
2 years ago
3
Not clear what the flag -p does
#27
maxozo
closed
2 years ago
2
application in scATAC-seq data
#26
zhijunyuu
closed
2 years ago
6
Large 10x bam files
#25
AnjaliC4
closed
2 years ago
3
cellsnp-lite runs indefinitely even on small BAM
#24
bradleycolquitt
closed
2 years ago
1
Update to v1.2.1
#23
hxj5
closed
2 years ago
0
mode 1b query -
#22
bjstewart1
closed
2 years ago
4
Clarification on demuxing with vcf
#21
cnk113
closed
3 years ago
1
mouse+human multiplexed
#20
AnjaliC4
closed
2 years ago
1
minor update
#19
hxj5
closed
3 years ago
0
Understand AD matrix
#18
Zepeng-Mu
closed
3 years ago
2
Run stalling?
#17
dpcook
closed
3 years ago
2
minor update
#16
hxj5
closed
3 years ago
0
installation issue
#15
AnjaliC4
closed
3 years ago
2
Use autotools for compilation
#14
hxj5
closed
3 years ago
0
update doc and add rerun benchmarking scripts
#13
hxj5
closed
3 years ago
0
update manual and fix compiling issue
#12
hxj5
closed
3 years ago
0
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