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ccmbioinfo
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crg2
Research pipeline for exploring clinically relevant genomic variants
Apache License 2.0
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Include analysis id in output directory
#181
Madelinehazel
closed
9 months ago
0
Update documentation
#180
Madelinehazel
closed
9 months ago
1
added function to decompress .ora files
#179
anjalijain22
closed
1 year ago
0
Refactor Phenotips functions
#178
Madelinehazel
closed
1 year ago
0
remove END and SVTYPE cols
#177
Madelinehazel
closed
1 year ago
0
add MELT to crg2
#176
ShaniaWu
closed
1 year ago
0
gene coverage: Python version of get_gene_exon_intron.R (pt.2)
#175
ShaniaWu
closed
1 year ago
0
gene coverage: Python version of get_gene_exon_intron.R
#174
ShaniaWu
closed
1 year ago
0
fix gene coverage README description
#173
ShaniaWu
closed
1 year ago
0
Dark region annotation for PacBio hg38 pipeline
#172
anjalijain22
closed
1 year ago
0
Gene coverage scripts
#171
ShaniaWu
closed
1 year ago
0
Pxu/fix gene search
#170
pamelaxu213
closed
1 year ago
0
Replace symbolic INS with N
#169
Madelinehazel
closed
1 year ago
0
Remove duplicates from cram instead of bam
#168
Madelinehazel
closed
1 year ago
0
Genome re-analysis
#167
Madelinehazel
closed
1 year ago
0
Annotate de novo report with hpo terms for GenomeRounds
#166
Madelinehazel
closed
1 year ago
0
Use samtools REF_CACHE to decompress CRAM
#165
Madelinehazel
closed
1 year ago
0
Convert BAM to CRAM
#164
Madelinehazel
closed
1 year ago
0
Crg2 hg38
#163
Madelinehazel
opened
1 year ago
0
Upload mosaic report to minio
#162
Madelinehazel
closed
1 year ago
0
Mutect2 exome-wide calling to detect mosaic variants
#161
Madelinehazel
closed
1 year ago
0
PT-G4RD Data Upload
#160
anjalijain22
closed
1 year ago
0
Mosaic panel
#158
pamelaxu213
closed
1 year ago
0
changed cre deleted database path to central annotations directory
#157
NourHanafi
closed
2 years ago
1
Updating the crg2-hg38 branch
#156
NourHanafi
closed
2 years ago
0
Write units and samples tsv even if ped does not validate
#155
Madelinehazel
closed
2 years ago
0
Fix EHDN files path
#154
Madelinehazel
closed
2 years ago
0
SV report fixes
#153
Madelinehazel
closed
2 years ago
1
Mitochondrial pipeline - Mity
#152
anjalijain22
closed
2 years ago
1
Merge SV report branch with SNV/indel report branch
#151
Madelinehazel
closed
2 years ago
0
Automated analyses with multiple datasets from the same individual
#150
Madelinehazel
opened
2 years ago
0
Automate coverage report generation for exomes
#149
Madelinehazel
closed
2 years ago
0
Remove hpf hardcoded values for ehdn
#148
Madelinehazel
closed
2 years ago
0
Pxu/ped check
#147
pamelaxu213
closed
2 years ago
1
Check dup script prints sample name + dup rate for all samples
#146
anjalijain22
closed
2 years ago
0
Add fastq regex
#145
Madelinehazel
closed
2 years ago
0
Modified BQSR compression level to 5
#144
anjalijain22
closed
2 years ago
0
Specify cre path
#143
Madelinehazel
closed
2 years ago
0
EHDN and EHDN report rules have hardcoded hpf paths and no environment
#142
Madelinehazel
opened
2 years ago
0
Mosaic workflow
#141
pamelaxu213
closed
1 year ago
0
Specify path to reference fasta when calling cre/cre.sh
#140
Madelinehazel
closed
2 years ago
0
Fix database path
#139
Madelinehazel
closed
2 years ago
0
Add cre database path as argument
#138
Madelinehazel
closed
2 years ago
0
BQSR doubles bam size
#137
Madelinehazel
closed
2 years ago
2
Slurm profile for CHEO-RI and Stager integration
#136
Madelinehazel
closed
1 year ago
6
Upload BND report to MinIO
#135
NourHanafi
closed
2 years ago
0
Pxu/fix ped
#134
pamelaxu213
closed
2 years ago
0
vcfanno "Info Error/Warning" for ClinVar Annotations
#133
anjalijain22
opened
2 years ago
0
Fix to accept mixed input types
#132
anjalijain22
closed
2 years ago
1
fix_ped
#131
pamelaxu213
closed
2 years ago
0
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