openvax isovar issues - Githubissues

openvax / isovar

Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence

Apache License 2.0

25 stars 13 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Use another genome/annotation?

#123 dining-philosopher opened 3 years ago
0
Can I specify which ensembl release to use by the isovar command line?

#122 nknewnew opened 3 years ago
0
added top_gene_name to IsovarResult and removed python 2.7 from Travis

#121 iskandr closed 4 years ago
1
RNA sequencing coverage

#120 nknewnew opened 4 years ago
0
WIP: Create mutant protein sequence object

#119 iskandr closed 4 years ago
0
get more than the top protein sequence

#118 drna opened 4 years ago
1
Add subsequence method ProteinSequence

#117 iskandr closed 4 years ago
1
Weird chromosome bug in MT variant under GRCh38

#116 iskandr opened 5 years ago
0
Faster assembly

#115 iskandr closed 4 years ago
0
Fix mismatch count after variant

#114 iskandr closed 5 years ago
1
Multiple phasing types

#113 iskandr closed 5 years ago
0
Normalize counts by number of mapped reads to get CPM

#112 iskandr opened 5 years ago
0
Speed up locus read construction

#111 iskandr closed 5 years ago
0
num_cdna_mismatches_after_variant_in_top_protein_sequence always non-zero

#110 iskandr closed 5 years ago
0
use list.index instead of dictionary construction to speed up LocusRead construction

#109 iskandr closed 5 years ago
0
added module for explicit phasing of somatic phasing

#108 iskandr closed 5 years ago
0
Exit early if no reference contexts for variant

#107 iskandr closed 5 years ago
0
Only want IsovarResults with protein sequences that differ from reference to pass filters

#106 iskandr closed 5 years ago
0
use varcode's effects() helper to get handling of intergenic effects

#105 iskandr closed 5 years ago
1
Major rewrite to enable use of newer pysam, fix several bugs, and add filtering options

#104 iskandr closed 5 years ago
1
Threshold ratio of alt alleles to all other non-ref alleles

#103 iskandr closed 5 years ago
1
Count read names and not just reads

#102 iskandr closed 5 years ago
0
Isovar with pysam > 0.9.0

#101 monikasekelja closed 5 years ago
2
Constructing wildtype peptides

#100 felixfrenkel opened 6 years ago
3
Variant sequence ... shorter than min allowed

#99 gilhornung opened 6 years ago
0
Run integration tests

#98 iskandr closed 6 years ago
0
make all the CLI tools use the same logic for generating/parsing output args

#97 iskandr closed 6 years ago
1
Refactor CLI

#96 iskandr closed 6 years ago
1
setup error: No such file or directory: 'isovar/__init__.py'

#95 gilhornung closed 6 years ago
4
option --use-duplicate-reads is ignores by isovar-protein-sequences.py

#94 drna closed 5 years ago
1
ASE for Synonymous + Non-synonymous Variants

#93 JPFinnigan opened 6 years ago
3
No exon_id in mouse mm9 ensembl annotaiotn

#92 weizhu365 opened 6 years ago
0
Isovar on multiple .bam

#91 JPFinnigan opened 6 years ago
1
Unexpectedly short protein sequences

#90 iskandr opened 6 years ago
9
Too slow running isovar. Could it be run in multithread?

#89 Jemimacat opened 6 years ago
0
Questions about Isovar

#88 iskandr opened 6 years ago
0
User wants "hg19" as genome option

#87 iskandr opened 6 years ago
0
By default, removing soft-clipped bases.

#86 julia326 closed 7 years ago
2
AssertionError deep in the stack

#85 julia326 closed 7 years ago
2
Figure out what to do when variant and transcript don't match

#84 julia326 opened 7 years ago
0
Fix variant reading into intron

#83 julia326 closed 7 years ago
4
Exception when deletion extends beyond exon boundary

#82 julia326 closed 7 years ago
0
Variant effect has a null `aa_mutation_start_offset`

#81 julia326 opened 7 years ago
1
Locus read rewrite

#80 iskandr closed 5 years ago
2
Left align indels

#79 iskandr opened 7 years ago
0
Exposing --include-mismatches-after-variant as a translation flag.

#78 julia326 closed 7 years ago
1
Expose flag to include mismatches after the variant

#77 julia326 closed 7 years ago
0
Incrementing the minor version, after the mismatches-after-variant change

#76 julia326 closed 7 years ago
2
Cut a new release

#75 julia326 closed 7 years ago
0
Optionally filter by number of mismatches after the variant

#74 julia326 closed 7 years ago
2