brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.

brentp/smoove Issues

svtyper: error: unrecognized arguments: --max_ci_dist 0 error
Closed 3 months ago1
library error in smoove
Updated 3 months ago4
issue with installation smoove via conda
Closed 4 months ago4
smoove genotype - could not import: bam_hdr_destroy
Updated 5 months ago3
lumpy_filter not on $PATH
Updated 5 months ago1
only histo file outputs from smoove call
Updated 5 months ago5
Failed to open -: unknown file type, panic
Updated 5 months ago5
【need help】An error occurred when running to Merge
Updated 6 months ago2
A bug when installing smoove with conda
Closed 6 months ago4
smoove paste error
Updated 7 months ago5
Multiple issues
Updated 8 months ago
Why REF = N?
Updated 8 months ago
using multiple bams from same sample - does not finish running & trims the sequencing run number from the sample name
Closed 8 months ago1
`--name` parameter does not work
Closed 8 months ago3
When I use smoove annotate, I just receive a MSHQ/SHQ of -1
Updated 8 months ago12
pre-processing for split & discordant read-pairs?
Closed 9 months ago1
smoove call fails immediately with Panic: unexpected EOF
Updated 9 months ago2
Polyploidy
Updated 10 months ago3
Different genotype of SV for the same sample in different batch
Updated 10 months ago
panic: open /path/to/*.bam: no such file or directory
Closed a year ago2
Run smoove for single sample?
Closed a year ago4
lumpy filter remove too much reads
Updated a year ago6
non-SV filtering
Updated a year ago2
No INS records
Closed a year ago1
sanity checks for sorted and RGs
Updated a year ago1
Smoove not working !!!!!! Failed to read from standard input: unknown file type panic: write |1: broken pipe
Updated a year ago5
Docker image missing svtyper
Updated a year ago
smoove calls huge number of calls
Closed a year ago2
samtools index: failed to create index for *mybamfile* panic: exit status 1
Closed a year ago1
bcftools: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory > gsort version 0.1.4
Closed a year ago2
[smoove] 2022/11/15 10:20:53 starting with version 0.2.8 [smoove] 2022/11/15 10:20:53 lumpy executable not found in PATH
Closed a year ago2
missing pair end parameters:mean stdev
Closed a year ago1
runtime: failed to create new OS thread
Closed a year ago4
Question about Exclude region
Closed 2 years ago3
libcrypto.so.1.0.0: cannot open shared object file error with biocontainers
Closed 2 years ago9
smoove duphold error
Updated 2 years ago3
important_regions bed
Closed 2 years ago2
Error while running smoove call: panic: sam: reference already used
Updated 2 years ago5
Error while running smoove genotype: "panic: fork/exec $PATH/bin/svtyper: too many open files"
Closed 2 years ago4
Smoove Call panic exit segmentation violation followed by unknown file type
Closed 2 years ago2
panic:gzip: invalid header
Updated 2 years ago8
panic: sam: duplicate program name: line 3430: "@PG\tID:SAMBLASTER\tVN:0.1.24\tCL:samblaster -i dummy.cram.readsorted.sam -o dummy.cram.samblster.sam --addMateTags"
Updated 2 years ago4
Error reading index file from S3 bucket
Updated 2 years ago2
"Missing pair end parameters:mean stdev" and histo files are empty.
Closed 2 years ago8
IMPRECISE Confuse
Closed 2 years ago2
mosdepth error
Closed 2 years ago2
Error in lumpy-filter
Closed 2 years ago5
gff format for GRCh38
Updated 2 years ago3
panic: parsing time during smoove call
Updated 2 years ago6
"hangup" error
Updated 2 years ago2