cortes-ciriano-lab/SComatic

Issues

• Failure of installing pybedtools and rpy2

  #70 opened 2 months ago by LiuCanidk
  1

• Detecting somatic SNPs with VAF=1

  #71 opened a month ago by Swap90
  2

• Fig6 plot mutation data

  #69 opened 2 months ago by seoyounglee6445
  0

• Step4.2 fails to output any variants from scATACseq data

  #66 opened 3 months ago by archieandrews10
  5

• How to estimate single-cell mutational burdens

  #65 opened 3 months ago by xyzheng123
  3

• Plotting 96 trinucleotide mutation count

  #67 opened 3 months ago by hl-xue
  0

• pysam.pileup low max depth leads to FP

  #63 opened 3 months ago by ArthurDondi
  5

• Matching SNP to cell barcode

  #57 opened 3 months ago by malonzm1
  1

• output of SingleCellGenotype is empty!

  #61 opened 3 months ago by dipingxian431
  6

• start > stop

  #60 opened 3 months ago by xuxif
  1

• Issue while generating a custom PoN file

  #48 opened a year ago by Swap90
  2

• Using chromosome reference in Scomatic

  #62 opened 4 months ago by Arsamat
  1

• Issue with betabinomial estimation?

  #59 opened 6 months ago by danieljrichard
  1

• Problem installing SComatic

  #43 opened a year ago by malonzm1
  2

• The problem of analysing single-cell data from multiple tissues of the same individual

  #58 opened 7 months ago by zhoudreames
  1

• If the Scomatic could provide the variant allele frequency of unique cell

  #56 opened 8 months ago by luhuan93
  0

• how does input the tsv file to MutationalPatterns

  #55 opened 8 months ago by dipingxian431
  0

• How to remove the influence of different cell numbers

  #54 opened 9 months ago by xinghua1001
  0

• Understanding step 4.2 variant filters

  #53 opened 10 months ago by bkinnersley
  1

• TrinucleotideContextBackground.py - No such file or directory!

  #33 opened a year ago by lipikakalson
  16

• Two questions; about 'Cell_type_noise' filter and MT mutation calling

  #41 opened a year ago by leehs96
  1

• How does SingleCellGenotype.py work and what does it mean if substantial number of cell have different expected and observed cell types?

  #52 opened 10 months ago by prakashraaz
  0

• Mutational Burden Calculation

  #51 opened 10 months ago by JakeJackson22
  0

• minimal number of cells required for each cell type

  #50 opened 10 months ago by rosaranli
  0

• run SComatic with not FACS-sorted data

  #49 opened 10 months ago by giorgiagandolfi
  0

• Concurrent running of cells for step 2.

  #47 opened a year ago by JakeJackson22
  2

• Very low number of matched variants when comparing known SNVs from several studies with the results obtained by SComatic when applied to the same data

  #45 opened a year ago by FranSoriano
  4

• Does SComatic identify frameshift mutations?

  #46 opened a year ago by FranSoriano
  2

• Challenges with adapting for long read data?

  #38 opened a year ago by tsa4002
  2

• Why is the default value of the parameter "min_mq" 255

  #39 opened a year ago by Topigs
  1

• hg38 fa recommendation

  #42 opened a year ago by malonzm1
  1

• How to separate normal and cancer cells from the same cell type?

  #44 opened a year ago by cv55
  0

• SComatic with a single cell type but with germline reference

  #40 opened a year ago by northerngasc
  0

• Output of GetAllCallableSites.py for mutational burdens

  #23 opened a year ago by YiqunCao
  4

• A question about the script "BaseCellCalling.step1.py"

  #37 opened a year ago by sdzxzh
  0

• Do I need estimate new Beta binomial parameters for each sample? Another: according to somatic mutation in epi cells select cancer cell

  #36 opened a year ago by gloriafight
  0

• chromosome name difference, e.g., chr1 vs 1

  #27 opened a year ago by robinycfang
  2

• Split Bam Error 2

  #35 opened a year ago by sph17
  2

• Code for columns of the single cell level genotype result

  #30 opened a year ago by lijiang825
  5

• How to run the tool on multiple samples from the same patient

  #34 opened a year ago by MigleMi
  0

• ValueError: invalid coordinates: start > stop

  #28 opened a year ago by amdqiao1
  6

• How to convert to standard vcf format to be used for downstream analyses?

  #32 opened a year ago by lipikakalson
  1

• No base count matrix(.tsv) files in Step 2 output but bam files of those cell types are there in Step1 Output.

  #31 opened a year ago by lipikakalson
  16

• Run SComatic with a matched normal single-cell RNA-seq data

  #22 opened a year ago by gongyuTang123
  1

• When running scATAC data, No temporary files found in BaseCellCounter.py

  #29 opened a year ago by nieyage
  1

• Can you run SComatic on bulk RNA seq?

  #26 opened a year ago by sph17
  1

• How SComatic distinguishes between somatic and germline variants?

  #24 opened a year ago by vladimirkovacevic
  3

• package ‘VGAM’ is not available (for R version 3.6.1)

  #25 opened a year ago by FionaMoon
  1

• invalid contig `1`

  #20 opened a year ago by ramashka328
  4

• SComatic on Stereo-seq data

  #21 opened a year ago by vladimirkovacevic
  2