mgymrek/lobstr-code

Issues

• terminate called after throwing an instance of 'std::out_of_range'

  #92 opened 5 years ago by michaeldonaldson
  1

• lobstr_index.py can't build correctly index

  #80 opened 8 years ago by learniup
  1

• problem in documentation

  #97 opened 2 years ago by killtherealigo
  0

• Question about application in ancient DNA

  #96 opened 3 years ago by arenvale
  0

• I have 3000 samples of bam files to put in.

  #95 opened 3 years ago by wtfitis1
  0

• the proble of test

  #94 opened 4 years ago by xiaomiyang36
  0

• the

  #93 opened 4 years ago by GuanglinHe1
  2

• Heterzygosity calculation?

  #91 opened 6 years ago by wjaratlerdsiri
  0

• Make an hg38 reference

  #69 opened 9 years ago by mgymrek
  2

• lobSTR seems to fail when an N is located in the middle of the STR

  #90 opened 6 years ago by bkohrn
  0

• New g++5, boost. Lobsrt fails.

  #88 opened 7 years ago by tmozgach
  1

• MSI/MSS evaluation by using lobstr

  #87 opened 7 years ago by hanwenbogenecast
  0

• autoconf

  #77 opened 8 years ago by dwaggott
  3

• script lobSTR_filter_vcf.py failure

  #78 opened 8 years ago by aakrosh
  4

• lobstr is not compatible with cppunit 1.14!

  #84 opened 7 years ago by tmozgach
  0

• Bedtools v2.26.0 does not work with lobstr

  #83 opened 8 years ago by nh13
  0

• Support modern versions of BWA

  #82 opened 8 years ago by nh13
  0

• Building index failure

  #81 opened 8 years ago by learniup
  0

• Filtering lobSTR VCFs

  #79 opened 8 years ago by yclong8848
  0

• Fail to read read groups when PG is in header

  #72 opened 9 years ago by mgymrek
  1

• Program crashing on --command train

  #75 opened 8 years ago by holtgrewe
  1

• NoneType Errors running filter and vcf_to_tab scripts

  #76 opened 8 years ago by naymikm
  1

• Q score for heterozygous sites decreases with coverage

  #74 opened 9 years ago by mgymrek
  1

• allelotype: Process BAM files created by other aligners

  #55 opened 9 years ago by mgymrek
  0

• Duplicated read group IDs cause different samples to be merged

  #70 opened 9 years ago by mgymrek
  1

• Report Q scores in a log scale

  #66 opened 9 years ago by hdashnow
  1

• Starting with comma in alt field

  #67 opened 9 years ago by olekto
  0

• Ability to use existing RG information

  #63 opened 10 years ago by mgymrek
  0

• Only one value for multicopy STR markers reported

  #61 opened 10 years ago by trifud
  2

• Invalida FASTQ ID

  #51 opened 10 years ago by atks
  5

• ALLREADS flag discrepancy

  #60 opened 10 years ago by tfwillems
  4

• Allelotype help message

  #56 opened 10 years ago by tfwillems
  6

• Additional allelotype filter

  #52 opened 10 years ago by tfwillems
  1

• lobstr_index should give a clear warning if lobSTRIndex binary is not installed

  #33 opened 10 years ago by mgymrek
  2

• Extend parameter is hard coded in lobstr_index.py

  #50 opened 10 years ago by mgymrek
  1

• Multi-threading does not work on OSX

  #42 opened 10 years ago by mgymrek
  3

• Memory issue when running allelotype on OSX

  #37 opened 10 years ago by mgymrek
  2

• Convert reads to upper case before doing anything

  #43 opened 10 years ago by mgymrek
  0

• stats output sometimes does not produce full output

  #36 opened 11 years ago by mgymrek
  1

• Add documentation of the new reference set to the website

  #34 opened 11 years ago by mgymrek
  0

• scale negative side of step size PDF

  #32 opened 11 years ago by mgymrek
  1

• Alternate allele length of zero

  #30 opened 11 years ago by tfwillems
  1

• add post-alignment checks

  #20 opened 11 years ago by mgymrek
  3

• Don't use reads supporting invalid alleles to calculate genotype likelihoods

  #21 opened 11 years ago by mgymrek
  1

• Bug in BamTools::BamReader::GetTag() affecting allelotype.

  #23 opened 11 years ago by sunnybutterfly
  1

• Direction of read trimming in bam files

  #22 opened 11 years ago by mgymrek
  0

• Improve NW scoring

  #19 opened 11 years ago by mgymrek
  0

• Using --annotations gives negative PL scores

  #17 opened 11 years ago by mgymrek
  1

• BAM output for lobSTR in multi-threaded mode is truncated

  #14 opened 11 years ago by mgymrek
  1

• lobSTR bam output doesn't pass Picard ValidateSamFile.jar

  #9 opened 11 years ago by mgymrek
  1