arq5x lumpy-sv issues - Githubissues

arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

MIT License

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issues

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

#398 yqlan opened 3 weeks ago
0
windows for lumpyexpress

#397 licongge opened 1 month ago
0
run lumpy without speedseq

#396 RafigaM opened 2 months ago
0
Makefile - update BamTools to compile

#395 DavidStreid opened 3 months ago
0
Input BAM file not found

#394 espelpz opened 4 months ago
0
Missing pair end parameters:bamfile, histo_file, mean, stdev, read_length, min_non_overlap, discordant_z

#393 psardana22 opened 4 months ago
0
Lumpyexpress produces zero INS and CNV

#392 changhan1110 opened 1 year ago
1
Error reporting about 'make'

#391 zhaobinkai opened 1 year ago
2
lumpy ::claimsto be version (v 0.2.13)

#390 EricDeveaud opened 1 year ago
0
Can't find first and/or second of pair in sam block of length 2

#389 jonahcullen opened 1 year ago
0
ERROR in lumpyexpress -n: command not found; [: ==: unary operator expected

#388 ClarenceHsiang opened 1 year ago
5
File "/ME/alignment/lumpy-sv//scripts/bamkit/bamlibs.py", line 61 print ','.join(lib_rg[lib]) ^ SyntaxError: invalid syntax

#387 1580542426 opened 1 year ago
1
[E::idx_find_and_load] Could not retrieve index file for '-'

#386 liujiaxin7 opened 1 year ago
1
about out file

#385 linshengnan09 opened 1 year ago
0
make compile error

#384 sjads opened 1 year ago
5
parameter required for mean

#383 J-Bradlee opened 1 year ago
0
lumpy returns more than expected variants

#382 anoronh4 opened 2 years ago
0
BAM files must be coordinate sorted

#381 gneedle1 opened 2 years ago
1
Add batchx code

#380 idelvall closed 2 years ago
0
Error: -B is required

#379 khalidanaveed opened 2 years ago
0
some errors when do "make"

#378 gaom001 opened 2 years ago
1
Meaning of SU

#377 jsha129 closed 2 years ago
2
LUMPY SV caller on Low coverage WGS

#376 felipeluz97 opened 2 years ago
0
Can I get the copy number information?

#375 hayeon-pak closed 2 years ago
2
SV length

#374 cfz1998 closed 2 years ago
0
Output BAM with tags to associate reads back to SV calls?

#373 nh13 opened 2 years ago
1
Lumpy applicability

#372 anleopa opened 2 years ago
3
[E]lumpy-filter,error running command: set -eu;

#371 anxuan-web opened 2 years ago
2
lumpyexpress exited with "Could not retrieve index file for '-'"

#370 Ceonham opened 2 years ago
5
bam from samtools view -F 1294 is larger than bam from speedseq or

#369 liuhankui opened 2 years ago
3
Use of lumpy in haploid organisms

#368 pabloangulo7 opened 2 years ago
3
Question: construct contig that minimizes SVs

#367 JohnUrban opened 2 years ago
0
GT are all ./.

#366 meqili closed 2 years ago
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 ghost closed 2 years ago
0
where could i get hexdump?

#364 kztyes opened 2 years ago
0
lumpysxpress SyntaxError in input bam

#363 pedoman-GitHub opened 3 years ago
0
only use discordant reads

#362 Yiguan opened 3 years ago
2
lumpy Ouput vcf file

#361 u1200538 opened 3 years ago
1
lumpy not calling CNV

#360 kghimire09 opened 3 years ago
0
lumpyexpress error

#359 assane-mbodj opened 3 years ago
3
why there's SV that all samples showing reference allele

#358 shuiyanwu778 opened 3 years ago
5
Installation problem on mac Big sur

#357 kghimire09 opened 3 years ago
3
docs: specify whether output coordinates are 0 or 1 based

#356 amcpherson opened 3 years ago
4
Use single-end reads aligned with bwa-aln

#355 jcchacond opened 3 years ago
1
segment fault

#354 dfguan opened 3 years ago
0
Changing RG:Z flag in merged bam before lumpy

#353 markutz556 closed 3 years ago
0
Changing RG:Z flag when using merged bam files as input to lumpy

#352 markutz556 opened 3 years ago
0
genome file in bedpe_sort.py

#351 nitinra closed 3 years ago
0
Number of split reads supporting the variant is always 0

#350 yasin-uzun opened 3 years ago
18
choosing the right size for -b flad (breakpoint size) in cnvanator_to_bedpes.py

#349 nitinra closed 3 years ago
6