KolmogorovLab/Severus

Issues

• output-read-ids output unmatched variant id and read id

  #36 opened 2 months ago by lijunx33
  0

• explanation of TIN-ratio?

  #33 opened 2 months ago by apsteinberg
  4

• Typo in the get_segment function in bam_processing.py script

  #34 opened 2 months ago by JinHuan95
  1

• converting insertions to translocations

  #32 opened 2 months ago by eesiribloom
  1

• The number of somatic SVs is too less

  #35 opened 2 months ago by DayTimeMouse
  1

• How to choose phased.vcf ?

  #31 opened 2 months ago by DayTimeMouse
  1

• Question: distinction between DEL and DEL-like BND events

  #30 opened 2 months ago by ajw2329
  2

• How to understand the haplotags in the output file

  #29 opened 3 months ago by ywzhang071394
  2

• INFO/END is smaller than POS

  #11 opened 3 months ago by linsindian
  2

• Discrepancy in DEL Calls Between Severus Nanopore and PacBio Datasets for COLO829 Cell Line

  #13 opened 3 months ago by skeremaydin
  7

• Allow VNTR BED to be compressed

  #16 opened 3 months ago by awgymer
  2

• VNTRs

  #23 opened 3 months ago by minw2828
  4

• `<INV>` format

  #25 opened 5 months ago by awgymer
  3

• Redundant `CHR2` field

  #28 opened 4 months ago by awgymer
  1

• Incompatability of VACmap

  #26 opened 4 months ago by jamesc99
  2

• Hello @jamesc99 ,

  #27 opened 4 months ago by jamesc99
  0

• Insert ALT format

  #19 opened 4 months ago by awgymer
  7

• Sample IDs based on filenames causing errors in computation

  #20 opened 6 months ago by tdido
  3

• Haptype information in output files

  #24 opened 5 months ago by ywzhang071394
  2

• The reference sequence is masked with N

  #21 opened 7 months ago by DexinYang1998
  3

• COLO829 recall regression in v1.0

  #15 opened 9 months ago by proteinosome
  2

• Phasing with tumour-only long-reads as input for severus

  #18 opened 6 months ago by eesiribloom
  1

• Severus v1.0 much slower than v0.1.2 on COLO829

  #17 opened 6 months ago by RenzoTale88
  0

• Severus version is hardcoded in `source` field

  #22 opened 6 months ago by awgymer
  1

• severus for the tumor only mode

  #7 opened 9 months ago by qinqian
  9

• Phased bam from longshot

  #14 opened 10 months ago by kcleal
  2

• Calling without haplotagged alignments

  #12 opened 10 months ago by kcleal
  3

• Error in version 0.1.2

  #8 opened a year ago by proteinosome
  6

• Somatic SV breakpoint boundary issue caused by supplementary alignment boundaries

  #9 opened a year ago by aganezov
  1

• Missing somatic translocation/insertion SV breakpoint

  #10 opened a year ago by aganezov
  0

• pbmm2 no NM tag?

  #6 opened a year ago by jo-mc
  2

• Readme table columns swapped

  #5 opened a year ago by tbenavi1
  1