quinlan-lab/STRling

Issues

• Comparing STR length from STRling, which value would be appropriate to use?

  #121 opened 4 months ago by chanhee22kim
  0

• strling-outliers.py: Incompatibility with newer Pandas version

  #119 opened 4 months ago by ryanmcggg
  4

• Multiallelic STRs

  #120 opened 4 months ago by themkdemiiir
  1

• L.start <= R.start

  #113 opened a year ago by christopher-schroeder
  3

• Typo in command line help

  #118 opened 6 months ago by hdashnow
  0

• SIGSEGV: Illegal storage access. (Attempt to read from nil?)

  #114 opened 6 months ago by christopher-schroeder
  19

• STRling warning in [Joint call str loci across all samples]

  #117 opened 7 months ago by chanhee22kim
  2

• gene and variant scores

  #110 opened a year ago by naamaeb
  0

• Is it okay to apply STRling on PCR-based WGS dataset?

  #108 opened 2 years ago by a7420174
  9

• STRling warning message and empty binaries

  #107 opened 2 years ago by hdashnow
  0

• Assertion error for reads without sequence

  #103 opened 2 years ago by christopher-schroeder
  5

• Exclude NaN rows in STRs.tsv output

  #105 opened 2 years ago by hdashnow
  0

• 0-length intervals

  #104 opened 2 years ago by hdashnow
  0

• conda install error message (still installs)

  #86 opened 3 years ago by hdashnow
  1

• Issue with low proportion_repeat

  #102 opened 3 years ago by mhguo1
  7

• Binary build error

  #101 opened 3 years ago by hdashnow
  3

• How are allele sizes estimated?

  #99 opened 3 years ago by hchetia
  4

• SIGSEGV: Illegal storage access. (Attempt to read from nil?)

  #96 opened 3 years ago by hchetia
  3

• Output VCF

  #11 opened 5 years ago by hdashnow
  3

• Inconsistent soft-clipped reads may impact length estimates

  #93 opened 3 years ago by hdashnow
  0

• Support hemizygous calls in males on sex chromosomes

  #62 opened 4 years ago by hdashnow
  0

• Error: repeat not found in expected region

  #26 opened 3 years ago by danielecook
  8

• Set up verbose messages with logging

  #8 opened 3 years ago by hdashnow
  1

• Evaluate bounds soft-clip support using entropy

  #12 opened 5 years ago by hdashnow
  1

• SIGSEGV: Illegal storage access. (Attempt to read from nil?)

  #25 opened 3 years ago by bjtrost
  6

• Output bam file with relocated anchored STR mates

  #28 opened 3 years ago by hdashnow
  1

• align_length > 0 Assertion Error

  #43 opened 3 years ago by christopher-schroeder
  3

• Check versions of htslib and hts.nim

  #33 opened 3 years ago by hdashnow
  1

• Parsing issue with outliers.py

  #63 opened 3 years ago by jgunti-code
  4

• Full diploid genotypes for 2 short alleles

  #91 opened 3 years ago by seboyden
  1

• Typo and bug in the version warning?

  #38 opened 3 years ago by hdashnow
  1

• Checksum mismatch in cram decode

  #76 opened 4 years ago by nmmsv
  6

• STR ref subcommand

  #7 opened 4 years ago by hdashnow
  0

• Hide advanced parameters

  #20 opened 5 years ago by hdashnow
  0

• STRling version number is in two places

  #34 opened 5 years ago by hdashnow
  0

• Do some sensible filtering by default

  #52 opened 4 years ago by hdashnow
  0

• STRling merge error "SIGSEGV: Illegal storage access" when -l bed is used

  #58 opened 4 years ago by hdashnow
  0

• Homopolymer false positives

  #53 opened 4 years ago by hdashnow
  11

• Need a more useful error for when bed file chromosomes don't match reference genome

  #54 opened 4 years ago by hdashnow
  0

• Add a sample input file

  #24 opened 5 years ago by hdashnow
  1

• Call stage has high memory utilization for large numbers of bounds

  #32 opened 5 years ago by hdashnow
  1

• assign_reads_locus produces bad indices

  #35 opened 5 years ago by hdashnow
  2

• Combine equivalent STR repeat units for unplaced reads?

  #5 opened 5 years ago by hdashnow
  0

• Add bounds filtering settings as command line options

  #17 opened 5 years ago by hdashnow
  1

• Unexpectedly high number of anchored reads reported

  #14 opened 5 years ago by hdashnow
  3

• Off by 1 errors when detecting if a read spans a locus?

  #6 opened 5 years ago by hdashnow
  13

• recode homopolymers

  #3 opened 5 years ago by hdashnow
  2

• For cases where we are uncertain about the bounds, look at the reference genome sequence

  #4 opened 5 years ago by hdashnow
  0