REPRODUCIBILITY: Comparing lg3 2019-03-23 to previous versions

[HenrikBengtsson]

Comparing lg3 2019-03-23 Patient157t10 results to those of lg3 2018-10-08 gives:

[cbctest2@n17 lg3-demo-2019-03-23]$ module load CBC lg3/2019-03-23
[cbctest2@n17 lg3-demo-2019-03-23]$ LG3_TEST_TRUTH=../lg3-demo-2018-10-08/truth PATIENT=Patient157t10 lg3 test validate
*** Configuration
[OK] PROJECT=LG3
[OK] PATIENT=Patient157t10
[OK] CONV=patient_ID_conversions.tsv
[OK] LG3_TEST_TRUTH=../lg3-demo-2018-10-08/truth

*** Trimming of FASTQ Files
[OK] file tree ('output/LG3/trim/Z00*-trim')
[OK] file sizes ('output/LG3/trim/Z00*-trim/*')

*** BWA Alignment of FASTQ Files
[OK] file tree ('output/LG3/exomes')
[OK] file sizes ('output/LG3/exomes/Z00*/*')

*** Recalibration of BAM Files
[OK] file tree ('output/LG3/exomes_recal/Patient157t10')
[OK] file sizes ('output/LG3/exomes_recal/Patient157t10/*')
[OK] file sizes ('output/LG3/exomes_recal/Patient157t10/germline/*')
[OK] file sizes ('output/LG3/exomes_recal/Patient157t10/*.bai')

*** Pindel Processing
[OK] file tree ('output/LG3/pindel')
[OK] file rows ('output/LG3/pindel/Patient157t10.pindel.cfg')
[OK] file sizes ('output/LG3/pindel/Patient157t10_pindel/*')

*** MutDet Processing
[OK] file tree ('output/LG3/mutations/Patient157t10_mutect')
[OK] file sizes ('output/LG3/mutations/Patient157t10_mutect/*')

*** Post-MutDet Processing
[OK] file tree ('output/LG3/MAF')
[OK] file sizes ('output/LG3/MAF/Patient157t10_MAF/*')
[OK] file sizes ('output/LG3/MAF/Patient157t10_plots/*')
[OK] file tree ('output/LG3/MutInDel')
[OK] file sizes ('output/LG3/MutInDel/*')
[OK] file content ('output/LG3/MutInDel/Patient157t10.R.mutations')

[HenrikBengtsson]

Comparing lg3 2019-03-23 Patient157t10 results to those of lg3 2018-12-17 gives:

[cbctest2@n17 lg3-demo-2019-03-23]$ module load CBC lg3/2019-03-23
[cbctest2@n17 lg3-demo-2019-03-23]$ LG3_TEST_TRUTH=../lg3-demo-2018-12-27/truth PATIENT=Patient157t10 lg3 test validate
*** Configuration
[OK] PROJECT=LG3
[OK] PATIENT=Patient157t10
[OK] CONV=patient_ID_conversions.tsv
[OK] LG3_TEST_TRUTH=../lg3-demo-2018-12-27/truth

*** Trimming of FASTQ Files
[OK] file tree ('output/LG3/trim/Z00*-trim')
[OK] file sizes ('output/LG3/trim/Z00*-trim/*')

*** BWA Alignment of FASTQ Files
[OK] file tree ('output/LG3/exomes')
[OK] file sizes ('output/LG3/exomes/Z00*/*')

*** Recalibration of BAM Files
[OK] file tree ('output/LG3/exomes_recal/Patient157t10')
[OK] file sizes ('output/LG3/exomes_recal/Patient157t10/*')
[OK] file sizes ('output/LG3/exomes_recal/Patient157t10/germline/*')
[OK] file sizes ('output/LG3/exomes_recal/Patient157t10/*.bai')

*** Pindel Processing
[OK] file tree ('output/LG3/pindel')
[OK] file rows ('output/LG3/pindel/Patient157t10.pindel.cfg')
[OK] file sizes ('output/LG3/pindel/Patient157t10_pindel/*')

*** MutDet Processing
[OK] file tree ('output/LG3/mutations/Patient157t10_mutect')
[WARN] unexpected file sizes ('../lg3-demo-2018-12-27/truth/Patient157t10/output/LG3/mutations/Patient157t10_mutect/*' != 'output/LG3/mutations/Patient157t10_mutect/*')
@@ -6,2 +6,2 @@
-69M    output/LG3/mutations/Patient157t10_mutect/NOR-Z00599t10__REC1-Z00601t10.snvs.coverage.mutect.bed
-615M   output/LG3/mutations/Patient157t10_mutect/NOR-Z00599t10__REC1-Z00601t10.snvs.coverage.mutect.wig
+70M    output/LG3/mutations/Patient157t10_mutect/NOR-Z00599t10__REC1-Z00601t10.snvs.coverage.mutect.bed
+622M   output/LG3/mutations/Patient157t10_mutect/NOR-Z00599t10__REC1-Z00601t10.snvs.coverage.mutect.wig
@@ -14,2 +14,2 @@
-87M    output/LG3/mutations/Patient157t10_mutect/NOR-Z00599t10__TUM-Z00600t10.snvs.coverage.mutect.bed
-617M   output/LG3/mutations/Patient157t10_mutect/NOR-Z00599t10__TUM-Z00600t10.snvs.coverage.mutect.wig
+88M    output/LG3/mutations/Patient157t10_mutect/NOR-Z00599t10__TUM-Z00600t10.snvs.coverage.mutect.bed
+626M   output/LG3/mutations/Patient157t10_mutect/NOR-Z00599t10__TUM-Z00600t10.snvs.coverage.mutect.wig

*** Post-MutDet Processing
[OK] file tree ('output/LG3/MAF')
[OK] file sizes ('output/LG3/MAF/Patient157t10_MAF/*')
[OK] file sizes ('output/LG3/MAF/Patient157t10_plots/*')
[OK] file tree ('output/LG3/MutInDel')
[OK] file sizes ('output/LG3/MutInDel/*')
[OK] file content ('output/LG3/MutInDel/Patient157t10.R.mutations')