single-cell-genetics/cellsnp-lite

Issues

• Generating Single VCF file for Each scRNA-Seq Sample

  #125 opened a month ago by hkarakurt8742
  3

• 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 opened 8 months ago by jiehuichen
  4

• UMI Collapsing

  #121 opened 3 months ago by grasshoffm
  5

• Matching SNPs to cell barcode

  #124 opened 2 months ago by malonzm1
  0

• Unable to install through anaconda

  #120 opened 3 months ago by Angelos-Gk
  7

• Combined max depth is above 1M. Potential memory hog! / Recommendations for maxDepth?

  #122 opened 3 months ago by bbimber
  2

• [E::bgzf_flush] File write failed (wrong size)

  #117 opened 3 months ago by ghuls
  2

• Could not retrieve index file for .bam

  #119 opened 3 months ago by nansne
  3

• runtime and expected output

  #78 opened 2 years ago by ahoffrichter
  6

• Strand specificity

  #118 opened 4 months ago by flde
  1

• Integrating mouse SNPs and scRNA-seq data for imprinted gene identification

  #115 opened 5 months ago by singcell
  0

• The 19 of 20 parallelized workers always strike far before the whole job is done

  #88 opened a year ago by mimi3421
  3

• Converting cellsnp-lite outputs to vartrix's consensus matrix

  #114 opened 6 months ago by mdmanurung
  1

• Is there a good way to identify and add the gene names to the output vcfs?

  #113 opened 7 months ago by pchatterjee7
  1

• Use cellSNP on a big BAM file

  #111 opened 7 months ago by RosaDeSa
  1

• minimal minor allele count filter?

  #108 opened 8 months ago by chilampoon
  2

• How to check the real reads cover an SNP in a cell?

  #107 opened 8 months ago by jiehuichen
  4

• cellsnp-lite on data from 1 donor

  #106 opened 8 months ago by astaburuaga-garcia
  2

• get unwanted allele in ALT column

  #105 opened 9 months ago by jiehuichen
  2

• 10x scATAC-seq like bam file, No reads captured with "--UMItag None"

  #104 opened 9 months ago by jiehuichen
  5

• the resulting file has only the title and no content

  #102 opened 10 months ago by suhuanhou
  6

• OTH ratio 1

  #93 opened a year ago by flde
  5

• scRNA-seq from different donors as a genotype-vcf input for vireo

  #100 opened a year ago by mariafiruleva
  6

• -ldeflate is missing in Makefile after I executed ./configure

  #98 opened a year ago by darkcircle
  0

• postprocessing cellsnp outputs

  #96 opened a year ago by maxozo
  1

• miscount alleles single-cell ATAC-seq

  #95 opened a year ago by raul-w
  4

• Error when using more than 2 bam files with mode 1B

  #94 opened a year ago by cameronyoungpark
  5

• Question for minMAF parameter

  #77 opened 2 years ago by fe4960
  5

• Filter SNPs by minMAF after running cellsnp-lite

  #90 opened a year ago by flde
  8

• Application to Slide-seq V2 returns empty vcf

  #91 opened a year ago by kzb193
  3

• How to use cellsnp-lite

  #89 opened a year ago by DaliBAmor
  1

• Handling haploid cells

  #87 opened a year ago by haigdjambazian
  2

• more reads filter options?

  #85 opened a year ago by zhentaoyoung
  4

• Genotyping ATAC from WES vcf

  #86 opened a year ago by ollieeknight
  5

• hg38 chromsome names in 1000G VCF and 10X BAM

  #84 opened a year ago by jnktsj
  2

• Duplicate barcodes error?

  #80 opened a year ago by terencewtli
  2

• Barcodes File Clarification

  #81 opened a year ago by DarioS
  3

• AF for candidate SNP

  #66 opened 2 years ago by Zepeng-Mu
  2

• Incorrect output when using BD Rhapsody / STAR solo input

  #79 opened 2 years ago by sbamopoulos
  2

• Automatically detect all chromosomes in bam

  #76 opened 2 years ago by chilampoon
  2

• single cell RNA-seq cellsnp lite error mode 2b+ 1a

  #75 opened 2 years ago by drlaurenwasson
  1

• Unable to install CellSNP-Lite from conda

  #74 opened 2 years ago by aseyedia
  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 opened 2 years ago by honghh2018
  1

• how can i build the preprocess vcf for mouse, like human common SNP vcf file, using GATK google warehouse snp data

  #72 opened 2 years ago by honghh2018
  1

• ELBO plot decreasing instead of increasing to a plateau

  #71 opened 2 years ago by haigdjambazian
  2

• Huge 10X scRNA-seq mouse data

  #70 opened 2 years ago by alexfernandes8a
  1

• Filtering cells before or after cellsnp-lite

  #68 opened 2 years ago by haigdjambazian
  1

• The mutation matrix input for SCITE

  #69 opened 2 years ago by alanfoleynibrt
  0

• How to set -p (Slurm)

  #67 opened 2 years ago by flde
  1

• Calling SNPs using multiple bam files with single cell data

  #65 opened 2 years ago by scachero
  5