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AH - implement changes for mitochondrial pipeline #6399

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merged 85 commits into from
Apr 22, 2020
Merged

AH - implement changes for mitochondrial pipeline #6399

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f9133ab
initial impl
ahaessly Nov 19, 2019
49875a6
start impl
ahaessly Nov 19, 2019
e94059e
wip
ahaessly Dec 5, 2019
22345ad
converted base qual and tumor
ahaessly Dec 6, 2019
32d4ed2
converted mapping qual filter
ahaessly Dec 6, 2019
1d64edf
updated duplicate alt read filter - but need to add tests
ahaessly Dec 6, 2019
8b85de2
undo bad delim change
ahaessly Dec 6, 2019
27b49be
update min allele fraction filter
ahaessly Jan 3, 2020
1568a0e
update read pos filter
ahaessly Jan 6, 2020
2b045c0
2 different get data methods
ahaessly Jan 6, 2020
409aff2
use correct filter list
ahaessly Jan 7, 2020
e54983c
fix issues with filters containing data for ref
ahaessly Jan 7, 2020
9f78917
wip, doens't pass tests, fixing error prob for threshold
ahaessly Jan 10, 2020
8e0e7d4
implement 2 pass variant walker as post processing filter step for lo…
ahaessly Jan 13, 2020
660c4f9
wip - got error prob to compile
ahaessly Jan 14, 2020
eb2a590
wip - fixed almost all compile errors
ahaessly Jan 14, 2020
9938a54
wip almost done - one more q for DB
ahaessly Jan 14, 2020
63c4147
fixed some bugs
ahaessly Jan 14, 2020
e934453
mito filter tests pass
ahaessly Jan 14, 2020
5d75607
add AS_SB_Table as mutect2 annotation
ahaessly Jan 15, 2020
1e35952
made strict strand bias allele specific
ahaessly Jan 15, 2020
f347db5
add test data for AS_SB_TABLE in vcf. format not compatible with anno…
ahaessly Jan 16, 2020
c7efe6e
convert stand artifact - bug with prior list
ahaessly Jan 16, 2020
4344277
fixed strand artifact - fix and verify tests
ahaessly Jan 16, 2020
f11171f
fix bug in strand artifact. still need tests
ahaessly Jan 17, 2020
72d87ab
strand artifact - use total from all alleles
ahaessly Jan 17, 2020
6bf1ecf
put AS_SB_TABLE back into gvcf format
ahaessly Jan 17, 2020
781064a
fix bug in strict strand filter that was ignoring the minReadsOnEachS…
ahaessly Jan 21, 2020
6f19cc3
minor changes
ahaessly Jan 21, 2020
d9318c0
remove generic from Mutect2AlleleFilter and make generic methods stat…
ahaessly Jan 21, 2020
ec8f63c
minor changes and comments
ahaessly Jan 21, 2020
b5e207a
update from PR feedback
ahaessly Jan 23, 2020
03754fc
changes after rebase and to test FAIL filter
ahaessly Jan 24, 2020
98a9dc8
fix issue with null value for SB annotation
ahaessly Jan 24, 2020
c8bdeee
fix output files for test
ahaessly Jan 24, 2020
fb956fb
remove warnings
ahaessly Jan 24, 2020
5de3575
update splitting alleles to include analyzing AS_FilterStatus and set…
ahaessly Jan 30, 2020
2cb9b5c
fix extra spaces in filter list
ahaessly Jan 30, 2020
53d31a0
Fixed AF and SB splitting; also some javadoc I should have done in the
ldgauthier Jan 31, 2020
9446699
fix warning, fixes from PR feedback
ahaessly Feb 3, 2020
d6f9006
fix another generics issue
ahaessly Feb 3, 2020
ffecce7
make unique alt read count allele specific
ahaessly Feb 3, 2020
4fc762b
fix genotypes not included in vcf
ahaessly Feb 4, 2020
0deea4c
better test for low het filter
ahaessly Feb 7, 2020
03aefbf
changed getRequiredAnnotations to getRequiredInfoAnnotations to be mo…
ahaessly Feb 7, 2020
851a90c
fix low het filter to ignore ref AF
ahaessly Feb 12, 2020
9e59a3f
remove . in AS_FilterStatus for ref, and change PASS to .
ahaessly Feb 12, 2020
5459d4f
fix bug in removing symbolic data
ahaessly Feb 14, 2020
30b59dc
add test for uniq alt read count
ahaessly Feb 18, 2020
e702456
add final tests
ahaessly Feb 18, 2020
ff2051e
fix error in LeftAlignAndTrim after rebase
ahaessly Feb 20, 2020
fc585da
fix as splitting in left align and trim...
ahaessly Feb 20, 2020
343cd5f
updated test for split multi allelics
ahaessly Feb 21, 2020
4697b02
needed to update another test file
ahaessly Feb 21, 2020
94fa473
fix split multiallelics to work for all info fields
ahaessly Mar 4, 2020
8091e0d
change count type for RPA
ahaessly Mar 5, 2020
30396ad
make NuMTFilter its own tool. update constants for MT low het tool
ahaessly Mar 5, 2020
a3ed2d3
change info field count type back to 1, since format is non-standard
ahaessly Mar 9, 2020
39d04a7
fix test
ahaessly Mar 9, 2020
8205932
change allele specific filter status of . to SITE
ahaessly Mar 9, 2020
54bd5db
more output for failing test
ahaessly Mar 9, 2020
6b496b8
make MT filter low het tool allele specific
ahaessly Mar 12, 2020
711ae07
update the passing indicator to SITE
ahaessly Mar 17, 2020
2068a78
use already computed AF instead of recomputing in MT Low het tool
ahaessly Mar 18, 2020
3ae2795
get tests working
ahaessly Mar 23, 2020
a9ab22c
final mods
ahaessly Mar 23, 2020
3076777
minor change
ahaessly Mar 23, 2020
10a4ba7
fix expected files
ahaessly Mar 24, 2020
74fff72
update to lastest wdl
ahaessly Mar 25, 2020
272f6b8
cleanup
ahaessly Mar 30, 2020
35ab284
updating wdl
ahaessly Mar 31, 2020
0dfab1d
fix bug that removes existing filters
ahaessly Apr 1, 2020
9b8f211
add one more test
ahaessly Apr 1, 2020
3b43c10
fix overwrite of filter
ahaessly Apr 1, 2020
8191f3c
add missing test files
ahaessly Apr 2, 2020
54b7fc1
should fix wdl tests
ahaessly Apr 3, 2020
37c8c81
fix wdl tests
ahaessly Apr 3, 2020
4dcd088
fix path
ahaessly Apr 3, 2020
d6b1229
fix path again
ahaessly Apr 6, 2020
e60ed86
remove blacklisted shifted
ahaessly Apr 6, 2020
717d87f
add error checking for contam file format
ahaessly Apr 7, 2020
69cca57
minor refactor
ahaessly Apr 14, 2020
f51ba10
update example inputs to use broad public bucket for refs
ahaessly Apr 15, 2020
59f3dc9
doc updates
ahaessly Apr 16, 2020
33c2942
update documentation
ahaessly Apr 21, 2020
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5 changes: 4 additions & 1 deletion scripts/m2_cromwell_tests/run_m2_wdl.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,9 @@ cd $WORKING_DIR/gatk/scripts/
sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" m2_cromwell_tests/test_m2_wdl_multi.json >$WORKING_DIR/test_m2_wdl_multi_mod.json
echo "JSON FILE (modified) ======="
cat $WORKING_DIR/test_m2_wdl_multi_mod.json
sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" m2_cromwell_tests/test_mitochondria_m2_wdl.json >$WORKING_DIR/test_mitochondria_m2_wdl_mod.json
echo "JSON FILE (modified) ======="
cat $WORKING_DIR/test_mitochondria_m2_wdl_mod.json
echo "=================="

# Create the tumor-only json by using the pair_list_tumor_only file
Expand All @@ -52,4 +55,4 @@ sudo java -jar $CROMWELL_JAR run $WORKING_DIR/gatk/scripts/mutect2_wdl/mutect2_m
echo "Running Mitochondria M2 WDL through cromwell"
ln -fs $WORKING_DIR/gatk/scripts/mitochondria_m2_wdl/AlignAndCall.wdl
ln -fs $WORKING_DIR/gatk/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl
sudo java -jar $CROMWELL_JAR run $WORKING_DIR/gatk/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl -i $WORKING_DIR/gatk/scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json -m $WORKING_DIR/test_mitochondria_m2_wdl.metadata
sudo java -jar $CROMWELL_JAR run $WORKING_DIR/gatk/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl -i $WORKING_DIR/test_mitochondria_m2_wdl_mod.json -m $WORKING_DIR/test_mitochondria_m2_wdl.metadata
3 changes: 1 addition & 2 deletions scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
{
"MitochondriaPipeline.gatk_docker_override": "__GATK_DOCKER__",
"MitochondriaPipeline.wgs_aligned_input_bam_or_cram": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/NA12878.alignedHg38.duplicateMarked.baseRealigned.bam",
"MitochondriaPipeline.wgs_aligned_input_bam_or_cram_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/NA12878.alignedHg38.duplicateMarked.baseRealigned.bam.bai",
"MitochondriaPipeline.autosomal_coverage": 30,
Expand All @@ -21,8 +22,6 @@
"MitochondriaPipeline.mt_shifted_bwt": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.bwt",
"MitochondriaPipeline.mt_shifted_pac": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.pac",
"MitochondriaPipeline.mt_shifted_sa": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.sa",
"MitochondriaPipeline.blacklisted_sites_shifted": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.shifted_by_8000_bases.bed",
"MitochondriaPipeline.blacklisted_sites_shifted_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.shifted_by_8000_bases.bed.idx",
"MitochondriaPipeline.shift_back_chain": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/ShiftBack.chain",
"MitochondriaPipeline.control_region_shifted_reference_interval_list": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/control_region_shifted.chrM.interval_list",
"MitochondriaPipeline.non_control_region_interval_list": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/non_control_region.chrM.interval_list"
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