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populationgenomics
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joint-calling
Sample and variant QC, based on https://github.com/broadinstitute/gnomad_qc
MIT License
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Renames get_sequences_by_sample_ids to *_for_sample_ids
#92
illusional
closed
1 year ago
2
Add NA12878 validation notebook
#91
vladsavelyev
closed
2 years ago
0
Fix license description
#90
lgruen
closed
2 years ago
0
[join-calling]: use transmitted singletons
#89
vladsavelyev
opened
2 years ago
0
[large-cohort] Document variant filtering
#88
vladsavelyev
opened
2 years ago
0
[population pipeline] NAGIM: prepare amp-pd+mgrb subset for Joe Copty
#87
vladsavelyev
opened
2 years ago
0
[population pipeline] Benchmark NAGIM run
#86
vladsavelyev
opened
2 years ago
1
Make release VCF. Nagim. Support relateds. SM 4.0.0. Add X het/hom ratio and freqs
#85
vladsavelyev
closed
2 years ago
0
Update sm api
#84
vivbak
closed
1 year ago
0
Fix no value for param
#83
vivbak
closed
2 years ago
0
PCA plots: use external IDs, fix double counting
#82
vladsavelyev
closed
2 years ago
0
Update PCA plots, fix PED file, check existence flags
#81
vladsavelyev
closed
2 years ago
0
Incorporate gene names into hover tools.
#80
KatalinaBobowik
closed
2 years ago
0
Add Somalier for relatedness checks
#79
vladsavelyev
closed
2 years ago
0
Move more requester-pay files & fix in PCA plot
#78
vladsavelyev
closed
2 years ago
0
Fix Unit Tests
#77
vivbak
closed
2 years ago
1
Move requester-pays ref files
#76
vladsavelyev
closed
2 years ago
0
Add validation samples. Add alignment and haplotypecaller.
#75
vladsavelyev
closed
2 years ago
0
Integrate ancestry
#74
vladsavelyev
closed
3 years ago
1
Sample QC refactoring (mostly `pc_relate`)
#73
vladsavelyev
closed
3 years ago
0
Split `sample_qc.py` into `sample_qc_calculate.py` and `sample_qc_write_metadata.py`
#72
vladsavelyev
closed
3 years ago
0
Sample QC: use non-preemptible workers
#71
vladsavelyev
closed
3 years ago
0
Fix setting up workers disk
#70
vladsavelyev
closed
3 years ago
0
More disk for sample_qc
#69
vladsavelyev
closed
3 years ago
0
Add tmp dir for VQSR
#68
vladsavelyev
closed
3 years ago
0
More space for Apply VQSR job
#67
vladsavelyev
closed
3 years ago
0
Various SM communication fixes
#66
vladsavelyev
closed
3 years ago
0
Run joint-calling from this repo rather than tob-wgs
#65
vladsavelyev
closed
3 years ago
0
Read data from the SM server
#64
vladsavelyev
closed
3 years ago
0
Fix merge
#63
vivbak
closed
3 years ago
0
Fix reads
#62
vivbak
closed
3 years ago
0
Fix Request
#61
vivbak
closed
3 years ago
0
Add 300 cap
#60
vivbak
closed
3 years ago
0
Split mt, add `snps_not_on_gnomad`, move ref files
#59
vladsavelyev
closed
3 years ago
1
remove sm_project, replace with project
#58
vivbak
closed
3 years ago
0
Pull latest inputs using SM API
#57
vivbak
closed
3 years ago
1
Broad issue to track the joint-calling workflow improvement
#56
vladsavelyev
opened
3 years ago
0
Fix md5 check
#55
vivbak
closed
3 years ago
0
Fix according to analysis runner update
#54
vivbak
closed
3 years ago
0
Matrix table output updates
#53
vladsavelyev
closed
3 years ago
1
Add storage for hl.export_vcf
#52
vladsavelyev
closed
3 years ago
0
Integrate sample metadata API
#51
vivbak
closed
3 years ago
3
Refactor docstrings
#50
vladsavelyev
closed
3 years ago
0
ReblockGVCFs: keep low quals
#49
vladsavelyev
closed
3 years ago
0
Validate MD5
#48
vivbak
closed
3 years ago
0
Add comment about spanning del, fix `AS_SB_TABLE` parsing, fix overwriting
#47
vladsavelyev
closed
3 years ago
0
Refactor mt_to_vcf
#46
vladsavelyev
closed
3 years ago
2
Fix & refactor combining with existing matrix table
#45
vladsavelyev
closed
3 years ago
0
Write metadata to new metadata buckets
#44
vladsavelyev
closed
3 years ago
0
Adapt upload processor to new metadata buckets
#43
lgruen
closed
3 years ago
0
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