eldariont/svim issues and pull requests

#71 - samtools error

Issue - State: open - Opened by ajbarley 5 months ago

#70 - svim2.0.0 err

Issue - State: open - Opened by vegetableyu 10 months ago

#69 - all.vcf did not contain BND and insertion sequences

Issue - State: open - Opened by makise58 about 1 year ago

#68 - INV score not calculating

Issue - State: open - Opened by avictorsen over 1 year ago

#67 - bioconda install

Issue - State: open - Opened by Noczio over 1 year ago

#66 - pos of interspersed duplication

Issue - State: open - Opened by bakeronit over 1 year ago - 1 comment

#65 - Error question. Please delete.

Issue - State: closed - Opened by leone93 almost 2 years ago

#64 - Multi-sample processing

Issue - State: open - Opened by YahGao almost 2 years ago - 1 comment

#63 - Start position

Issue - State: open - Opened by Akazhiel over 2 years ago

#62 - Fail to get the svim_evaluation.zip

Issue - State: open - Opened by SQLiu-youyou over 2 years ago

#61 - [BUG] Unsorted positions on sequence

Issue - State: open - Opened by Irallia over 2 years ago - 2 comments

#60 - Problem with DUP naming. SVLEN is not present in INV calls.

Issue - State: open - Opened by mldmort almost 3 years ago

#59 - how many calls should we expect?

Issue - State: closed - Opened by woodoo46 about 3 years ago - 5 comments

#58 - SVIM 2.0.0 in conda

Issue - State: open - Opened by Akazhiel about 3 years ago - 3 comments

#57 - Reads supporting BND events

Issue - State: closed - Opened by Akazhiel about 3 years ago - 2 comments

#56 - Reference allele missing

Issue - State: open - Opened by Akazhiel about 3 years ago - 2 comments

#55 - Add output name options

Issue - State: open - Opened by Akazhiel about 3 years ago - 1 comment

#54 - Reversed start and end of BND

Issue - State: closed - Opened by charliechen912ilovbash about 3 years ago - 1 comment

#53 - Confusion about output

Issue - State: closed - Opened by cgrootcrego over 3 years ago - 2 comments

#52 - Understand the output?

Issue - State: closed - Opened by wenbinmei over 3 years ago - 1 comment

#51 - parameter settings for more support reads

Issue - State: closed - Opened by yekaizhou over 3 years ago - 4 comments

#50 - Low number of interspersed duplications?

Issue - State: closed - Opened by GuillaumeHolley over 3 years ago - 1 comment

#49 - Improved Documentation

Issue - State: closed - Opened by CharlesARoy over 3 years ago - 2 comments

#48 - population call with svim

Issue - State: closed - Opened by Chenglin20170390 over 3 years ago - 3 comments

#47 - merge the two lines translocation(BND) records into one line

Issue - State: closed - Opened by charliechen912ilovbash over 3 years ago - 2 comments

#46 - The genotype of the variants.vcf file were ./.

Issue - State: closed - Opened by Xuelei-Dai over 3 years ago - 1 comment

#45 - SVIM tries to use deprecated Numpy feature

Issue - State: closed - Opened by InvisOn over 3 years ago - 1 comment

#44 - using svim alignment to genotype, all the tandem duplications show missing value

Issue - State: open - Opened by lx-4199 over 3 years ago - 1 comment

#43 - svim alignment error

Issue - State: closed - Opened by lukaslee1127 almost 4 years ago - 1 comment

#42 - what is the recommended annotation tools after SV calling?

Issue - State: closed - Opened by charliechen912ilovbash almost 4 years ago - 2 comments

#41 - the recommended sequencing depth

Issue - State: closed - Opened by charliechen912ilovbash almost 4 years ago - 2 comments

#40 - Is SVIM suitable for detecting somatic SV?

Issue - State: closed - Opened by charliechen912ilovbash almost 4 years ago - 1 comment

#39 - Alignment pipeline error

Issue - State: closed - Opened by camilogarciabotero almost 4 years ago - 8 comments

#38 - Underflow on variant position?

Issue - State: closed - Opened by wdecoster almost 4 years ago - 5 comments

#37 - MemoryError

Issue - State: closed - Opened by Boer223 about 4 years ago - 3 comments

#36 - (Almost) no insertions

Issue - State: closed - Opened by LizzieMcDizzie over 4 years ago - 5 comments

#35 - raw reads or corrected reads ?

Issue - State: closed - Opened by ptranvan over 4 years ago - 1 comment

#34 - ERROR when using assembly-vs-assembly BAM as input

Issue - State: closed - Opened by biozzq over 4 years ago - 3 comments

#33 - Check existence of bam index upfront

Issue - State: closed - Opened by SHuang-Broad over 4 years ago - 2 comments

#32 - [Feature request] Expose CLI for customizing batch size

Issue - State: closed - Opened by SHuang-Broad over 4 years ago - 1 comment

#31 - Phasing interpretation

Issue - State: closed - Opened by javibio-git over 4 years ago - 4 comments

#30 - SVIM breaks with OSError: truncated file in Genotyping step

Issue - State: closed - Opened by caspargross over 4 years ago - 2 comments

#29 - FORMAT 'CN' is not defined in the header

Issue - State: closed - Opened by zihhuafang over 4 years ago - 3 comments

#28 - SV types in output VCF

Issue - State: closed - Opened by shimbalama over 4 years ago - 3 comments

#27 - pysam error

Issue - State: closed - Opened by ndierckx over 4 years ago - 8 comments

#26 - Understanding the scoring?

Issue - State: closed - Opened by alelim-bio almost 5 years ago - 4 comments

#25 - complex events detection

Issue - State: closed - Opened by jiadong324 almost 5 years ago - 3 comments

#24 - Wrong SVLEN values

Issue - State: closed - Opened by ricardovialle almost 5 years ago - 4 comments

#23 - Suggestion: Add BEDPE as an optional output

Issue - State: closed - Opened by Dfupa almost 5 years ago - 4 comments

#22 - Q: is it possible to allow users choose between NGMLR Minimap2?

Issue - State: closed - Opened by SHuang-Broad almost 5 years ago - 4 comments

#21 - issue when reading sam/bam of empty SEQ field

Issue - State: closed - Opened by xp3i4 about 5 years ago - 2 comments

#20 - bam index not found

Issue - State: closed - Opened by webbchen about 5 years ago - 5 comments

#19 - Problem with installing through conda

Issue - State: closed - Opened by SHuang-Broad about 5 years ago - 6 comments

#18 - Can the software detecting cnvs, differing from the dup.tandom and dup.interspered?

Issue - State: closed - Opened by forrwill about 5 years ago - 5 comments

#17 - ModuleNotFoundError: No module named 'svim'

Issue - State: closed - Opened by niccw about 5 years ago - 2 comments

#16 - Sequences of insertion

Issue - State: closed - Opened by Edison2021 about 5 years ago - 4 comments

#15 - Error at stage of GENOTYPE

Issue - State: closed - Opened by Edison2021 over 5 years ago - 2 comments

#14 - Using SVIM for the detection of large somatic SVs

Issue - State: closed - Opened by hr283 over 5 years ago - 8 comments

#13 - error with /bin/sh and set -o pipefail

Issue - State: closed - Opened by curtisjamison over 5 years ago - 1 comment

#12 - Can I run SVIM with multi threads?

Issue - State: open - Opened by tjiangHIT over 5 years ago - 8 comments

#11 - Use case of your SVIM software

Issue - State: closed - Opened by anandksrao over 5 years ago - 3 comments

#10 - undefined info in header

Issue - State: closed - Opened by wdecoster over 5 years ago - 7 comments

#9 - order of reads in bam file

Issue - State: closed - Opened by wdecoster over 5 years ago - 3 comments

#8 - local variable 'end2' referenced before assignment

Issue - State: closed - Opened by SAMtoBAM over 5 years ago - 6 comments

#7 - Long Walltime?

Issue - State: closed - Opened by dantaki almost 6 years ago - 4 comments

#6 - Real world benchmarks

Issue - State: closed - Opened by armintoepfer almost 6 years ago - 8 comments

#5 - Accept coordinate sorted alignments

Issue - State: closed - Opened by armintoepfer almost 6 years ago - 3 comments
Labels: enhancement

#4 - Git tag for 0.3.1?

Issue - State: closed - Opened by stain almost 6 years ago - 1 comment

#3 - Suggestion/Request: add to PyPI and/or bioconda

Issue - State: closed - Opened by wdecoster over 6 years ago - 2 comments
Labels: enhancement

#2 - Define contigs in the header

Issue - State: closed - Opened by wdecoster over 6 years ago - 1 comment

#1 - error with gzipped fastq file and create working dir if it doesn't exist

Issue - State: closed - Opened by wdecoster over 6 years ago - 2 comments

GitHub / eldariont/svim issues and pull requests