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update VRS annotation batch script for v4 exomes #382

Merged
merged 26 commits into from
Aug 24, 2023
Merged

update VRS annotation batch script for v4 exomes #382

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fd1b874
copy vrs from v3 to v4
KoalaQin Jul 20, 2023
2776164
add v4 exomes to input & output
KoalaQin Jul 20, 2023
417a49f
add note for faster hadoop_ls after Hail 0.2.119
KoalaQin Jul 20, 2023
d1e7807
make vcf2ht Hail Batch step
KoalaQin Jul 21, 2023
031e24e
simply vcf to HT in annotate-original
KoalaQin Jul 21, 2023
247d1e7
simplify final HT annotation
KoalaQin Jul 21, 2023
6a9a56d
minor changes
KoalaQin Jul 21, 2023
d64f8f8
modify exclude duplicate
KoalaQin Jul 21, 2023
238632d
add note to hadoop_ls change
KoalaQin Jul 24, 2023
d05fcec
address Kristen's comments
KoalaQin Jul 31, 2023
fd256dc
rearrange code
KoalaQin Aug 15, 2023
f2092c1
remove deprecated parameter bucket in ServiceBackend
KoalaQin Aug 15, 2023
d4c5485
add test args to parse 200 partitions for testing
KoalaQin Aug 16, 2023
c9fc960
add input resource
KoalaQin Aug 16, 2023
8607b3d
keep up to date with main for annotations.py
KoalaQin Aug 16, 2023
604a308
add example command for backend and frontend use
KoalaQin Aug 16, 2023
2e0545f
rename the script file
KoalaQin Aug 16, 2023
cca5399
address reivew comments
KoalaQin Aug 23, 2023
60d6756
merge from origin/main
KoalaQin Aug 23, 2023
1758158
add params in get_vrs()
KoalaQin Aug 23, 2023
52c9a37
change to hl.struct for annotating VRS
KoalaQin Aug 23, 2023
cf0cba9
change input and output path
KoalaQin Aug 24, 2023
e8baf80
change input and output path
KoalaQin Aug 24, 2023
464932f
address review comments 2
KoalaQin Aug 24, 2023
40a253e
remove prefix and version as arguments
KoalaQin Aug 24, 2023
9f1d567
Update gnomad_qc/v4/annotations/vrs_annotation_batch.py
KoalaQin Aug 24, 2023
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