EichlerLab smrtsv2 issues

EichlerLab / smrtsv2

Structural variant caller

MIT License

53 stars 6 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

smrtsv2 support for ONT

#58 prasundutta87 closed 2 years ago
1
Smrtsv failed on polishing Pacbio CCS data in the assemble stage

#57 LYC-vio closed 2 years ago
2
how to use smrtsv2 on a aligned bam file

#56 masen1991 closed 3 years ago
7
align step output comparison

#55 gkaur closed 3 years ago
1
Can't build conda deps.

#54 osowiecki closed 3 years ago
19
Fail in call_variants

#53 zihhuafang closed 4 years ago
1
Best way to run SMRT-SV Genotyper on large number of samples?

#52 jjfarrell closed 4 years ago
2
Canu v1.7 failing due to GNUplot dependency

#51 rorycraig337 closed 4 years ago
3
DRMAA error

#50 zihhuafang closed 4 years ago
4
Dependency make failure at canu

#49 ibharvey closed 4 years ago
7
Example of input for --cluster-params

#48 zihhuafang closed 4 years ago
2
Python problem

#47 woodoo46 closed 4 years ago
6
High False negative rate

#46 AyushSaxena closed 4 years ago
13
Unable to compile dependencies

#45 lcslyh closed 4 years ago
4
Locked Directories

#44 AyushSaxena closed 3 years ago
2
Failed to assemble

#43 AyushSaxena closed 4 years ago
0
Recommended `--exclude` BED in the detect step

#42 SHuang-Broad closed 4 years ago
1
Is the `Align` step required?

#41 SHuang-Broad closed 4 years ago
1
Misc small patches to make file

#40 SHuang-Broad closed 4 years ago
1
smrtsv genotype for an arbitrary VCF

#39 AyushSaxena closed 4 years ago
1
QUAL and GQ in vcf

#38 mesnger closed 5 years ago
1
Genotyping using short reads?

#37 holtgrewe closed 5 years ago
1
Insertions and duplications

#36 ggstatgen closed 5 years ago
3
'Wildcards' object has no attribute 'cpu' Failed to index reference

#35 rozaimirazali closed 5 years ago
2
Can I use smrtsv2 to call SV across different species?

#34 qiuyixmm closed 5 years ago
1
TypeError when Genotyping

#33 RSherman15 closed 5 years ago
2
Temp file not found when genotyping

#32 RSherman15 closed 5 years ago
1
Failed to assemble group(RuntimeError)

#31 jiey6596 closed 5 years ago
4
Commit to turn RepeatMasker off introduces buggy syntax

#30 RSherman15 closed 5 years ago
1
Accessing map value by index

#29 bioinfornatics closed 5 years ago
5
Runtime error in assemble step

#28 lamevan closed 5 years ago
9
Error in rule detect_stops_count_per_bin

#27 lamevan closed 5 years ago
4
GRCh37 callset release for the data in [Audano et al 2019]

#26 ggstatgen closed 5 years ago
1
'call' phase fails - no inversions?

#25 ggstatgen closed 5 years ago
2
How to run smrtsv2 with fastq/fasta files

#24 bioysu closed 5 years ago
1
[input file ] smrtsv.py detect parameter

#23 Xuelei-Dai closed 5 years ago
1
Extract alt allele sequence

#22 rmccoy7541 closed 5 years ago
1
Error in rule detect_gaps_annotate_coverage

#21 rozaimirazali closed 5 years ago
12
Bus error during detect_gaps_search

#20 rozaimirazali closed 5 years ago
1
Do smrtsv2 have resume capability?

#19 rozaimirazali closed 5 years ago
1
Killed job locked folder

#18 RSherman15 closed 5 years ago
3
Detect step using local python installation

#17 RSherman15 closed 5 years ago
19
Unable to index (error with snakemake)

#16 AyushSaxena closed 5 years ago
1
Failed assembly step

#15 bioysu closed 5 years ago
11
Rerunning specific batches

#14 RSherman15 closed 5 years ago
1
Failed at align step

#13 bioysu closed 5 years ago
3
RepeatMasker call and engine settings

#12 ggstatgen closed 5 years ago
4
Using nanopore data

#11 wdecoster closed 5 years ago
2
blasr error message during alignment stage

#10 rozaimirazali closed 5 years ago
3
--tempdir is an unrecognized argument

#9 rozaimirazali closed 5 years ago
1