arq5x/lumpy-sv

Issues

• Does lumpy filter out multiple alleles？

  #401 opened 2 months ago by hhd1008611
  0

• lumpy fails to call tandem duplications that are shorter than the sequencing read length

  #400 opened 2 months ago by ruomu-helix
  0

• Lumpyexpress memory issue

  #399 opened 3 months ago by jordimaggi
  0

• how are the options '-m', '-mw' and '-msw' defined?

  #398 opened 5 months ago by yqlan
  0

• windows for lumpyexpress

  #397 opened 6 months ago by licongge
  0

• run lumpy without speedseq

  #396 opened 6 months ago by RafigaM
  0

• [E::idx_find_and_load] Could not retrieve index file for '-'

  #386 opened 2 years ago by liujiaxin7
  1

• ERROR in lumpyexpress -n: command not found; [: ==: unary operator expected

  #388 opened 2 years ago by ClarenceHsiang
  5

• Makefile - update BamTools to compile

  #395 opened 8 months ago by DavidStreid
  0

• Input BAM file not found

  #394 opened 9 months ago by espelpz
  0

• Error reporting about 'make'

  #391 opened 2 years ago by zhaobinkai
  2

• make compile error

  #384 opened 2 years ago by sjads
  5

• Missing pair end parameters:bamfile, histo_file, mean, stdev, read_length, min_non_overlap, discordant_z

  #393 opened 9 months ago by psardana22
  0

• docs: specify whether output coordinates are 0 or 1 based

  #356 opened 4 years ago by amcpherson
  4

• why there's SV that all samples showing reference allele

  #358 opened 4 years ago by shuiyanwu778
  5

• File "/ME/alignment/lumpy-sv//scripts/bamkit/bamlibs.py", line 61 print ','.join(lib_rg[lib]) ^ SyntaxError: invalid syntax

  #387 opened 2 years ago by 1580542426
  1

• Lumpyexpress produces zero INS and CNV

  #392 opened a year ago by changhan1110
  1

• lumpy ::claimsto be version (v 0.2.13)

  #390 opened 2 years ago by EricDeveaud
  0

• Can't find first and/or second of pair in sam block of length 2

  #389 opened 2 years ago by jonahcullen
  0

• lumpyexpress exited with "Could not retrieve index file for '-'"

  #370 opened 3 years ago by Ceonham
  5

• lumpyexpress error

  #359 opened 4 years ago by assane-mbodj
  3

• about out file

  #385 opened 2 years ago by linshengnan09
  0

• parameter required for mean

  #383 opened 2 years ago by J-Bradlee
  0

• lumpy returns more than expected variants

  #382 opened 2 years ago by anoronh4
  0

• BAM files must be coordinate sorted

  #381 opened 2 years ago by gneedle1
  1

• Error: -B is required

  #379 opened 2 years ago by khalidanaveed
  0

• some errors when do "make"

  #378 opened 3 years ago by gaom001
  1

• Can I get the copy number information?

  #375 opened 3 years ago by hayeon-pak
  2

• Lumpy applicability

  #372 opened 3 years ago by anleopa
  3

• Meaning of SU

  #377 opened 3 years ago by jsha129
  2

• LUMPY SV caller on Low coverage WGS

  #376 opened 3 years ago by felipeluz97
  0

• Output BAM with tags to associate reads back to SV calls?

  #373 opened 3 years ago by nh13
  1

• SV length

  #374 opened 3 years ago by cfz1998
  0

• [E]lumpy-filter,error running command: set -eu;

  #371 opened 3 years ago by anxuan-web
  2

• To solve the problem of samtools errors like this ： “samtools view: writing to standard output failed: Broken pipe； samtools view: error closing standard output: -1 ”

  #365 opened 3 years ago
  0

• bam from samtools view -F 1294 is larger than bam from speedseq or

  #369 opened 3 years ago by liuhankui
  3

• Use of lumpy in haploid organisms

  #368 opened 3 years ago by pabloangulo7
  3

• GT are all ./.

  #366 opened 3 years ago by meqili
  2

• Question: construct contig that minimizes SVs

  #367 opened 3 years ago by JohnUrban
  0

• lumpy Ouput vcf file

  #361 opened 3 years ago by u1200538
  1

• where could i get hexdump?

  #364 opened 3 years ago by kztyes
  0

• lumpysxpress SyntaxError in input bam

  #363 opened 3 years ago by pedoman-GitHub
  0

• only use discordant reads

  #362 opened 3 years ago by Yiguan
  2

• lumpy not calling CNV

  #360 opened 3 years ago by kghimire09
  0

• Installation problem on mac Big sur

  #357 opened 4 years ago by kghimire09
  3

• Use single-end reads aligned with bwa-aln

  #355 opened 4 years ago by jcchacond
  1

• segment fault

  #354 opened 4 years ago by dfguan
  0

• Changing RG:Z flag in merged bam before lumpy

  #353 opened 4 years ago by markutz556
  0

• Changing RG:Z flag when using merged bam files as input to lumpy

  #352 opened 4 years ago by markutz556
  0

• genome file in bedpe_sort.py

  #351 opened 4 years ago by nitinra
  0