malariagen vector-tools issues

malariagen / vector-tools

Scripts, pipelines, docs to support data production work for MalariaGEN vector projects.

MIT License

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when computing chunk sizes combine_zarrs.py uses original dtype.

#51 hardingnj opened 4 years ago
0
modify combine_zarr.py to use attrs complete

#50 hardingnj opened 4 years ago
0
Add support for dtype changes and better chunk calc

#49 hardingnj opened 4 years ago
2
standardize chunking and allow passthrough of dtype and byteorder

#48 hardingnj opened 4 years ago
0
Relax rounding of divergence in `combine_qc_cohort_stats.py`

#47 leehart closed 5 years ago
0
WDL pipeline for phasing

#46 jonbrenas opened 5 years ago
0
merge variants fix

#45 hardingnj closed 5 years ago
0
merge_zarrs pipeline doesn't handle variants/field well

#44 hardingnj closed 5 years ago
0
Avoid multi-user issues in Snakemake pipelines

#43 leehart closed 5 years ago
3
Avoid Snakemake multi-user issues

#42 leehart closed 5 years ago
1
edits to combine_zarr script: support wider chunks

#41 hardingnj closed 5 years ago
2
modify `scripts/combine_zarr.py` to allow edit of length of chunks

#40 hardingnj opened 5 years ago
0
Add code for converting accessibility.h5 to zarr

#39 hardingnj opened 5 years ago
0
Add ag1000g data catalogs

#38 alimanfoo closed 5 years ago
2
Add logic to allow variants/* fields

#37 hardingnj closed 5 years ago
3
Amend Snakemake workflow for combine-zarr-sample-genotypes

#36 leehart opened 5 years ago
0
remove conda env

#35 hardingnj closed 5 years ago
0
Add the pipeline to phase parents and progeny.

#34 hardingnj closed 5 years ago
1
Add pipelines for phasing parents progeny and evaluation of set to this repo

#33 hardingnj opened 5 years ago
0
Add support for variants/{FIELD} in combine sample genotypes pipeline

#32 hardingnj closed 5 years ago
0
27 fix memory issues in contamination script

#31 hardingnj closed 5 years ago
0
fix typo

#30 hardingnj closed 5 years ago
0
use fancy indexing

#29 hardingnj closed 5 years ago
0
Updating deps

#28 hardingnj closed 5 years ago
0
estimate_contamination fix memory errors

#27 hardingnj closed 5 years ago
2
Add test for is file to use zarr zipstore

#26 hardingnj closed 5 years ago
0
Combine genotypes pipeline fails if user does not own file

#25 hardingnj closed 5 years ago
0
Update combine zarr pipeline (precursor to replicate QC)

#24 hardingnj closed 5 years ago
3
Move plot function call within indent block

#23 hardingnj closed 5 years ago
2
Halting due to insufficient variants to estimate contamination

#22 leehart closed 5 years ago
3
20 combine update

#21 hardingnj closed 5 years ago
0
combine-zarr-calldata needs better config

#20 hardingnj opened 5 years ago
0
All pipelines to dump vector tools submodule last commit hash

#19 hardingnj opened 5 years ago
2
initial work on replicate qc

#18 hardingnj closed 5 years ago
6
Pipeline to perform replicate QC

#17 hardingnj opened 5 years ago
0
Add scripts as inputs to QC snakemake pipeline

#16 alimanfoo opened 5 years ago
3
update env.yml

#15 hardingnj closed 5 years ago
0
Ignore 0/1 for mean, med, mode calculations

#14 hardingnj closed 5 years ago
0
Add genotype zarr suffix option

#13 hardingnj closed 5 years ago
0
Sample QC pipeline improvements TO DOs.

#12 hardingnj opened 5 years ago
5
Add new pipeline for merging genotype zip zarrs

#11 hardingnj closed 5 years ago
0
Add pipeline to merge genotype zipped zarr files

#10 hardingnj opened 5 years ago
1
migrating scripts from v-ops

#9 hardingnj closed 5 years ago
1
QC improvements/edits

#8 hardingnj closed 5 years ago
0
Update qc pipeline

#7 hardingnj closed 5 years ago
0
QC pipeline edits: split filters from main pipeline.

#6 hardingnj closed 5 years ago
0
Import mlwh query functions from vector-ops

#5 amakunin closed 5 years ago
2
"Stripes" on sex coverage ratio plots.

#4 amakunin opened 5 years ago
0
Implement qc pipeline for vector work

#3 hardingnj closed 5 years ago
14
Fill README

#2 amakunin opened 5 years ago
1