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feat: tnscope tga pcr indel model #1523

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de62484
add merge script
mathiasbio Nov 11, 2024
1605c8c
replace bcftools with custom script
mathiasbio Nov 11, 2024
35401bc
fix script
mathiasbio Nov 11, 2024
c99b1e6
update vcfpy
mathiasbio Nov 12, 2024
a34f0fc
black
mathiasbio Nov 12, 2024
b3d5271
add more docstrings and typehints
mathiasbio Nov 12, 2024
29e87a6
fix
mathiasbio Nov 12, 2024
be9373d
add RPA filter
mathiasbio Nov 12, 2024
bee17f0
attempt fix
mathiasbio Nov 12, 2024
870820b
update script
mathiasbio Nov 20, 2024
0bf6a27
fixes
mathiasbio Nov 21, 2024
c5da949
fix
mathiasbio Nov 21, 2024
f93d44e
fix
mathiasbio Nov 21, 2024
bfdd6e1
Merge branch 'develop' into merge_snv_variants_script
mathiasbio Nov 21, 2024
5b9d7c7
Merge branch 'merge_snv_variants_script' of github.com:Clinical-Genom…
mathiasbio Nov 21, 2024
2fab1f3
black
mathiasbio Nov 21, 2024
cd6ee22
revert
mathiasbio Nov 21, 2024
2a3dd7d
reformat
mathiasbio Nov 21, 2024
95c06ef
try
mathiasbio Nov 28, 2024
66e642c
fix
mathiasbio Nov 29, 2024
0862377
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Nov 29, 2024
ea4b5ce
rework bcftools filter
mathiasbio Nov 29, 2024
f60adac
black
mathiasbio Nov 29, 2024
3874a90
changelog
mathiasbio Nov 29, 2024
6b3fe6e
fix
mathiasbio Nov 29, 2024
e96a980
fix
mathiasbio Nov 29, 2024
68aeae1
new filter
mathiasbio Dec 10, 2024
24fd9a1
convert to list
mathiasbio Dec 10, 2024
13fab22
major refactor of filter logic
mathiasbio Dec 16, 2024
c66a66e
bug fixes
mathiasbio Dec 16, 2024
72cfbe1
fix
mathiasbio Dec 16, 2024
50fbc0a
fix
mathiasbio Dec 16, 2024
61aa1ab
test
mathiasbio Dec 16, 2024
28de8d4
fix
mathiasbio Dec 16, 2024
f3f5cb2
fix bug
mathiasbio Dec 16, 2024
3095fd9
fix
mathiasbio Dec 17, 2024
b2c62c6
black
mathiasbio Dec 17, 2024
d435039
update comments
mathiasbio Dec 17, 2024
eb46385
fix clinical and research filters
mathiasbio Dec 17, 2024
7c3a484
fix vardict tn hardfilters
mathiasbio Dec 18, 2024
0456b05
update vardict hardfilters
mathiasbio Dec 18, 2024
f29b271
remove pass and triallelic site prefilters
mathiasbio Dec 18, 2024
84dd929
fix bug
mathiasbio Dec 18, 2024
a4844b6
update script
mathiasbio Jan 15, 2025
40f9e19
change pcr indel model to hostile
mathiasbio Jan 15, 2025
78a3e9b
change pcr model specifically for tumor only tga
mathiasbio Jan 17, 2025
d0e00f1
changelog
mathiasbio Jan 17, 2025
f63a41a
add sentieon script
mathiasbio Jan 17, 2025
568e5dd
clean up found in, and adding custom section to header
mathiasbio Jan 20, 2025
94a4503
update
mathiasbio Jan 20, 2025
7108a33
add new rule
mathiasbio Jan 20, 2025
82857a4
add license
mathiasbio Jan 20, 2025
9d30b8f
format black sentieon script
mathiasbio Jan 20, 2025
7efbf41
test
mathiasbio Jan 20, 2025
7698e73
update
mathiasbio Jan 21, 2025
8469b0d
change script
mathiasbio Jan 21, 2025
3b8aede
fix
mathiasbio Jan 21, 2025
4d436d9
fix
mathiasbio Jan 21, 2025
b056a11
return MERGED filter
mathiasbio Jan 21, 2025
55edd9b
test
mathiasbio Jan 21, 2025
bdd3710
fix
mathiasbio Jan 21, 2025
14c134d
test
mathiasbio Jan 21, 2025
4707d16
fix
mathiasbio Jan 21, 2025
654cb98
fix
mathiasbio Jan 21, 2025
3a65a29
test
mathiasbio Jan 21, 2025
54dd105
test
mathiasbio Jan 21, 2025
1e7d7ce
fix
mathiasbio Jan 21, 2025
2372e2d
set merged
mathiasbio Jan 21, 2025
3c9dfc2
fix
mathiasbio Jan 21, 2025
f51638a
refactor
mathiasbio Jan 21, 2025
5d76ac0
test
mathiasbio Jan 21, 2025
d2ee89a
fix
mathiasbio Jan 21, 2025
cdba200
fix typehints
mathiasbio Jan 21, 2025
984f791
black etc
mathiasbio Jan 21, 2025
4c0ecab
refactor
mathiasbio Jan 21, 2025
d407e63
black
mathiasbio Jan 21, 2025
5dc899b
change script
mathiasbio Jan 21, 2025
654e996
change raw delivery vcf file for UMI and standard tga
mathiasbio Jan 21, 2025
805ff7e
changelog
mathiasbio Jan 21, 2025
8056694
refactor
mathiasbio Jan 21, 2025
ab8cc0e
start refactor
mathiasbio Jan 23, 2025
98fcee4
refactor continues
mathiasbio Jan 24, 2025
72ab2dc
propogate refactor to rules
mathiasbio Jan 24, 2025
a5b0247
fix model
mathiasbio Jan 24, 2025
25e97c7
bug fix
mathiasbio Jan 24, 2025
b30b667
clean up old code
mathiasbio Jan 24, 2025
41025e1
refactor constant
mathiasbio Jan 24, 2025
15a9d1a
add BioinfoTools constant to balsamic smk
mathiasbio Jan 24, 2025
229e763
remove umi param from general tga
mathiasbio Jan 24, 2025
2c64e95
removing unussed analysis workflow param
mathiasbio Jan 24, 2025
7edc4d6
refactor
mathiasbio Jan 24, 2025
8975592
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Jan 24, 2025
930d0ad
merge develop
mathiasbio Jan 24, 2025
b6632a9
fix
mathiasbio Jan 24, 2025
8636569
fix
mathiasbio Jan 24, 2025
39fcb05
fix clinical hard filters
mathiasbio Jan 27, 2025
c778a16
fix soft filter
mathiasbio Jan 27, 2025
8164e8e
refactor
mathiasbio Jan 27, 2025
aff2b8c
refactor names
mathiasbio Jan 27, 2025
6b5c1ce
fix pytest
mathiasbio Jan 27, 2025
2c4cc23
add new filter
mathiasbio Jan 27, 2025
c7b301e
add pytests
mathiasbio Jan 27, 2025
a598574
update test names
mathiasbio Jan 27, 2025
ff86e7d
remove unused function
mathiasbio Jan 27, 2025
4cc420e
black
mathiasbio Jan 27, 2025
c47fbd2
add new vardict filter
mathiasbio Jan 28, 2025
dff2a39
corrected vardict strandbias to be general
mathiasbio Jan 28, 2025
d66e4a2
add filter and mark it will be ignored
mathiasbio Jan 28, 2025
2d66075
remove filters that will be removed
mathiasbio Jan 28, 2025
85b2a20
updated docs
mathiasbio Jan 28, 2025
8490657
fix pytest
mathiasbio Jan 28, 2025
7e49b70
change logic of mnv filters
mathiasbio Jan 29, 2025
01fae23
Merge branch 'disable_normal_hardfilter' of github.com:Clinical-Genom…
mathiasbio Jan 29, 2025
a2390ae
merge with softfilter branch
mathiasbio Jan 29, 2025
44b11e9
fix filters
mathiasbio Jan 29, 2025
064a7b1
unpack set
mathiasbio Jan 29, 2025
b17c384
rename filter
mathiasbio Jan 29, 2025
8f0d7a2
change order of mnv processing
mathiasbio Jan 29, 2025
8dcc3c5
fix bug
mathiasbio Jan 29, 2025
ac6fe6f
fix bug
mathiasbio Jan 29, 2025
d2de191
add hard filter of MERGED variants
mathiasbio Jan 30, 2025
2dd995a
Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script
mathiasbio Jan 30, 2025
4cc5c9a
merge with other PRs
mathiasbio Jan 30, 2025
d9b2ff7
black
mathiasbio Jan 30, 2025
c15c8c9
add to docs
mathiasbio Jan 30, 2025
e51a537
Merge branch 'create_tnscope_mnvs' of github.com:Clinical-Genomics/BA…
mathiasbio Jan 30, 2025
4ca7fd6
Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script
mathiasbio Jan 30, 2025
b743d4d
fix filter
mathiasbio Jan 30, 2025
dd4b299
Merge branch 'create_tnscope_mnvs' of github.com:Clinical-Genomics/BA…
mathiasbio Jan 30, 2025
83f02a3
Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script
mathiasbio Jan 30, 2025
1282707
convert filter to infofield
mathiasbio Jan 31, 2025
6dbc9a3
bug fix
mathiasbio Jan 31, 2025
32844de
clean up
mathiasbio Jan 31, 2025
04bf774
try to fix
mathiasbio Jan 31, 2025
40895fd
testing
mathiasbio Jan 31, 2025
c05036b
change filter
mathiasbio Jan 31, 2025
d5de252
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Jan 31, 2025
ed2ea13
merge develop
mathiasbio Jan 31, 2025
e5c6e2e
fix
mathiasbio Feb 3, 2025
546bb46
Merge branch 'create_tnscope_mnvs' of github.com:Clinical-Genomics/BA…
mathiasbio Feb 3, 2025
38c6ebd
Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script
mathiasbio Feb 3, 2025
a89cecc
add pytests
mathiasbio Feb 3, 2025
6f75a5b
correct assert
mathiasbio Feb 3, 2025
625e9fa
add new assert
mathiasbio Feb 3, 2025
5cc8c2d
black
mathiasbio Feb 3, 2025
6a72ac2
fix
mathiasbio Feb 4, 2025
844ec59
refactor code
mathiasbio Feb 4, 2025
36b7eb6
black
mathiasbio Feb 4, 2025
3db1ebe
refactor
mathiasbio Feb 4, 2025
3b1a9a1
rename
mathiasbio Feb 4, 2025
4f97933
correct pytest
mathiasbio Feb 4, 2025
e3b0efe
Merge branch 'create_tnscope_mnvs' of github.com:Clinical-Genomics/BA…
mathiasbio Feb 4, 2025
e934b85
Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script
mathiasbio Feb 4, 2025
3c85260
refactor
mathiasbio Feb 5, 2025
8f628cb
fix
mathiasbio Feb 5, 2025
5f9a87f
fix
mathiasbio Feb 5, 2025
1776d41
fix
mathiasbio Feb 5, 2025
ac85443
fix tumor and normal af
mathiasbio Feb 5, 2025
520b08a
fix
mathiasbio Feb 5, 2025
8d9f6b3
fix
mathiasbio Feb 5, 2025
e3f5fa8
update docs
mathiasbio Feb 5, 2025
9919a55
remove file
mathiasbio Feb 5, 2025
2b71f38
remove file
mathiasbio Feb 5, 2025
76fcfbb
black
mathiasbio Feb 5, 2025
04d51fd
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Feb 5, 2025
b73d372
merge develop
mathiasbio Feb 5, 2025
ca88e5e
refactor names
mathiasbio Feb 5, 2025
02c1a28
fix
mathiasbio Feb 5, 2025
00331e0
Merge branch 'create_tnscope_mnvs' of github.com:Clinical-Genomics/BA…
mathiasbio Feb 6, 2025
87522b0
Merge branch 'create_tnscope_mnvs' into merge_snv_variants_script
mathiasbio Feb 6, 2025
85ed797
merge with merge script pr
mathiasbio Feb 6, 2025
74dff42
hostile conservative
mathiasbio Feb 13, 2025
d7ac281
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Feb 13, 2025
1942f5b
merge conflict
mathiasbio Feb 13, 2025
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2 changes: 1 addition & 1 deletion BALSAMIC/assets/scripts/edit_vcf_info.py
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ def edit_vcf_info(input_vcf, output_vcf, variant_caller):

with open(output_vcf, "wb"):
for variant in vcf:
variant.INFO["FOUND_IN"] = variant_caller + "|" + output_vcf
variant.INFO["FOUND_IN"] = variant_caller
new_vcf.write_record(variant)
new_vcf.close()
vcf.close()
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