single-cell-genetics cellsnp-lite issues

single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells

https://cellsnp-lite.readthedocs.io

Apache License 2.0

132 stars 11 forks source link

issues

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16,299 variants identified from mouse mtDNA chromosome in scRNAseq?

#141 jzussman opened 1 month ago
2
Do other species that adopt the 1a pattern need to specify chromosomes

#140 qiqi277 opened 1 month ago
1
Small doubt on preprocessing SNP data for mouse

#139 mauripops closed 1 month ago
3
long-read scRNA-seq

#138 Jiayi-Wang-Joey closed 2 months ago
4
Error with link to libhts.a

#137 NewtontheNeuron closed 2 months ago
2
Error: fail to write samples to cellSNP.samples.tsv

#136 Wenjun-Liu opened 3 months ago
1
Installation Error

#135 DarioS closed 3 months ago
2
cellsnp-lite on other species, organism

#134 dongwankimlab closed 3 months ago
2
Try to use the reads rather than UMIs for counting SNPs in spatial transcriptome (10x Visium)

#133 wJDKnight opened 3 months ago
5
How to detect all scaffolds (instead of chromosomes) in a bam file

#132 BrunaLuz opened 4 months ago
1
Issue with cellsnp-lite Running in Single-Thread Mode

#131 parv-sachdeva opened 4 months ago
1
HiC-pro mapping_combine.log: Failed to open file "XXX" : File exists

#130 leventLiu opened 4 months ago
1
0 variants found

#129 Sun-storm closed 4 months ago
8
update docs

#128 hxj5 closed 5 months ago
0
10X 5' single-cell data

#127 HenriettaHolze opened 5 months ago
4
Multiple Samples Per Individual Query

#126 sxf-ux closed 5 months ago
3
Generating Single VCF file for Each scRNA-Seq Sample

#125 hkarakurt8742 opened 6 months ago
3
Matching SNPs to cell barcode

#124 malonzm1 opened 6 months ago
0
Update docs and post-hoc analysis

#123 hxj5 closed 7 months ago
0
Combined max depth is above 1M. Potential memory hog! / Recommendations for maxDepth?

#122 bbimber closed 8 months ago
2
UMI Collapsing

#121 grasshoffm closed 8 months ago
5
Unable to install through anaconda

#120 Angelos-Gk opened 8 months ago
8
Could not retrieve index file for .bam

#119 nansne opened 8 months ago
3
Strand specificity

#118 flde opened 8 months ago
1
[E::bgzf_flush] File write failed (wrong size)

#117 ghuls closed 8 months ago
2
--help/--version should exit with status 0 (and write to stdout)

#116 jemma-nelson closed 9 months ago
1
Integrating mouse SNPs and scRNA-seq data for imprinted gene identification

#115 singcell opened 10 months ago
0
Converting cellsnp-lite outputs to vartrix's consensus matrix

#114 mdmanurung opened 10 months ago
1
Is there a good way to identify and add the gene names to the output vcfs?

#113 pchatterjee7 opened 11 months ago
1
Manual: major update

#112 hxj5 closed 11 months ago
0
Use cellSNP on a big BAM file

#111 RosaDeSa opened 1 year ago
1
improve documentation, fix readthedocs dependencies, initialize post-hoc analysis

#110 hxj5 closed 1 year ago
0
In a given SNP region, what are the criteria being used to categorize a cell as WT(0/0), heterozygote(1/0), and homozygote(1/1)?

#109 jiehuichen closed 1 year ago
4
minimal minor allele count filter?

#108 chilampoon closed 1 year ago
2
How to check the real reads cover an SNP in a cell?

#107 jiehuichen closed 1 year ago
4
cellsnp-lite on data from 1 donor

#106 astaburuaga-garcia opened 1 year ago
2
get unwanted allele in ALT column

#105 jiehuichen closed 1 year ago
2
10x scATAC-seq like bam file, No reads captured with "--UMItag None"

#104 jiehuichen closed 1 year ago
5
improve VCF header formatting

#103 hxj5 closed 1 year ago
0
the resulting file has only the title and no content

#102 suhuanhou opened 1 year ago
6
Fix support for "--doubletGL" argument.

#101 ghuls closed 1 year ago
4
scRNA-seq from different donors as a genotype-vcf input for vireo

#100 mariafiruleva opened 1 year ago
9
Add a proper VCF header to "cellSNP.base.vcf.gz".

#99 ghuls closed 1 year ago
0
-ldeflate is missing in Makefile after I executed ./configure

#98 darkcircle opened 1 year ago
0
csp_utils: sort mtx by 1st column first

#97 hxj5 closed 1 year ago
0
postprocessing cellsnp outputs

#96 maxozo opened 1 year ago
1
miscount alleles single-cell ATAC-seq

#95 raul-w closed 1 year ago
4
Error when using more than 2 bam files with mode 1B

#94 cameronyoungpark opened 1 year ago
5
OTH ratio 1

#93 flde opened 1 year ago
5
add csp_utils for post-processing outputs

#92 hxj5 closed 1 year ago
0