diff --git a/tests/data/README.md b/tests/data/README.md index 744e842f..707505d6 100644 --- a/tests/data/README.md +++ b/tests/data/README.md @@ -35,6 +35,8 @@ When adding a new module, please check carefully whether the data necessary for * 'test_genomic.gff3.gz': bgzipped-version * paf * 'test_cds_from_genomic.paf': PAF file for MT192765.1 genome + * table: + * 'test.table': Recalibration table generated with gatk4 BaseRecalibrator from 'test_paired_end.sorted.bam', using 'test.vcf.gz' as known sites. * vcf * 'test.vcf', 'test2.vcf': generated from 'test_paired_end.sorted.bam' using bcftools mpileup, call and filter * 'test3.vcf': generated from 'test_single_end.sorted.bam' using bcftools mpileup, call and filter @@ -50,5 +52,3 @@ When adding a new module, please check carefully whether the data necessary for * gtf: additional gtf file for STAR * vcf: several VCF files for tools using those, will be removed in the future * 'test.txt.gar.gz' exemplary tar file for the untar module - - diff --git a/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.bam b/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.bam index a7872cc4..c07b88dd 100644 Binary files a/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.bam and b/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.bam differ diff --git a/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.sorted.bam b/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.sorted.bam index 6463283d..9a6f9aa9 100644 Binary files a/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.sorted.bam and b/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.sorted.bam differ diff --git a/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.sorted.bam.bai b/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.sorted.bam.bai index 033f0769..74b4d069 100644 Binary files a/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.sorted.bam.bai and b/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.sorted.bam.bai differ diff --git a/tests/data/genomics/sarscov2/bam/test_paired_end.bam b/tests/data/genomics/sarscov2/bam/test_paired_end.bam index c24e367a..2afb6618 100644 Binary files a/tests/data/genomics/sarscov2/bam/test_paired_end.bam and b/tests/data/genomics/sarscov2/bam/test_paired_end.bam differ diff --git a/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam b/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam index 1752345a..85cccf14 100644 Binary files a/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam and b/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam differ diff --git a/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam.bai b/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam.bai index 12b6ba5a..0c6d5a96 100644 Binary files a/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam.bai and b/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam.bai differ diff --git a/tests/data/genomics/sarscov2/bam/test_single_end.bam b/tests/data/genomics/sarscov2/bam/test_single_end.bam index a0b8e81c..71818067 100644 Binary files a/tests/data/genomics/sarscov2/bam/test_single_end.bam and b/tests/data/genomics/sarscov2/bam/test_single_end.bam differ diff --git a/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam b/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam index e86eb955..4a2a37b5 100644 Binary files a/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam and b/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam differ diff --git a/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam.bai b/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam.bai new file mode 100644 index 00000000..4c62eab5 Binary files /dev/null and b/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam.bai differ diff --git a/tests/data/genomics/sarscov2/bam/test_unaligned.bam b/tests/data/genomics/sarscov2/bam/test_unaligned.bam index 549c324e..e1dbf733 100644 Binary files a/tests/data/genomics/sarscov2/bam/test_unaligned.bam and b/tests/data/genomics/sarscov2/bam/test_unaligned.bam differ diff --git a/tests/data/genomics/sarscov2/table/test.table b/tests/data/genomics/sarscov2/table/test.table new file mode 100644 index 00000000..fd94701d --- /dev/null +++ b/tests/data/genomics/sarscov2/table/test.table @@ -0,0 +1,1522 @@ +#:GATKReport.v1.1:5 +#:GATKTable:2:17:%s:%s:; +#:GATKTable:Arguments:Recalibration argument collection values used in this run +Argument Value +binary_tag_name null +covariate ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate +default_platform null +deletions_default_quality 45 +force_platform null +indels_context_size 3 +insertions_default_quality 45 +low_quality_tail 2 +maximum_cycle_value 500 +mismatches_context_size 2 +mismatches_default_quality -1 +no_standard_covs false +quantizing_levels 16 +recalibration_report null +run_without_dbsnp false +solid_nocall_strategy THROW_EXCEPTION +solid_recal_mode SET_Q_ZERO + +#:GATKTable:3:94:%d:%d:%d:; +#:GATKTable:Quantized:Quality quantization map +QualityScore Count QuantizedScore + 0 0 93 + 1 0 93 + 2 0 93 + 3 0 93 + 4 0 93 + 5 0 93 + 6 0 93 + 7 0 93 + 8 0 93 + 9 0 93 + 10 0 93 + 11 0 93 + 12 0 93 + 13 0 93 + 14 1858 14 + 15 0 93 + 16 0 93 + 17 0 93 + 18 0 93 + 19 0 93 + 20 0 93 + 21 283 21 + 22 0 93 + 23 0 93 + 24 0 93 + 25 0 93 + 26 0 93 + 27 1056 27 + 28 0 93 + 29 0 93 + 30 0 93 + 31 0 93 + 32 4530 32 + 33 0 93 + 34 0 93 + 35 0 93 + 36 19579 36 + 37 0 93 + 38 0 93 + 39 0 93 + 40 0 93 + 41 0 93 + 42 0 93 + 43 0 93 + 44 0 93 + 45 0 93 + 46 0 93 + 47 0 93 + 48 0 93 + 49 0 93 + 50 0 93 + 51 0 93 + 52 0 93 + 53 0 93 + 54 0 93 + 55 0 93 + 56 0 93 + 57 0 93 + 58 0 93 + 59 0 93 + 60 0 93 + 61 0 93 + 62 0 93 + 63 0 93 + 64 0 93 + 65 0 93 + 66 0 93 + 67 0 93 + 68 0 93 + 69 0 93 + 70 0 93 + 71 0 93 + 72 0 93 + 73 0 93 + 74 0 93 + 75 0 93 + 76 0 93 + 77 0 93 + 78 0 93 + 79 0 93 + 80 0 93 + 81 0 93 + 82 0 93 + 83 0 93 + 84 0 93 + 85 0 93 + 86 0 93 + 87 0 93 + 88 0 93 + 89 0 89 + 90 0 90 + 91 0 91 + 92 0 92 + 93 0 93 + +#:GATKTable:6:1:%s:%s:%.4f:%.4f:%d:%.2f:; +#:GATKTable:RecalTable0: +ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors +barcode1 M 25.0000 25.0126 27306 83.00 + +#:GATKTable:6:5:%s:%d:%s:%.4f:%d:%.2f:; +#:GATKTable:RecalTable1: +ReadGroup QualityScore EventType EmpiricalQuality Observations Errors +barcode1 14 M 14.0000 1858 78.00 +barcode1 21 M 21.0000 283 1.00 +barcode1 27 M 27.0000 1056 0.00 +barcode1 32 M 32.0000 4530 3.00 +barcode1 36 M 36.0000 19579 1.00 + +#:GATKTable:8:1384:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; +#:GATKTable:RecalTable2: +ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors +barcode1 14 -10 Cycle M 14.0000 4 1.00 +barcode1 14 -100 Cycle M 14.0000 12 0.00 +barcode1 14 -101 Cycle M 14.0000 9 0.00 +barcode1 14 -102 Cycle M 14.0000 7 0.00 +barcode1 14 -103 Cycle M 14.0000 6 0.00 +barcode1 14 -104 Cycle M 14.0000 6 1.00 +barcode1 14 -105 Cycle M 14.0000 7 0.00 +barcode1 14 -106 Cycle M 14.0000 4 0.00 +barcode1 14 -107 Cycle M 14.0000 3 0.00 +barcode1 14 -108 Cycle M 14.0000 10 1.00 +barcode1 14 -109 Cycle M 14.0000 5 0.00 +barcode1 14 -11 Cycle M 14.0000 1 0.00 +barcode1 14 -110 Cycle M 14.0000 12 1.00 +barcode1 14 -111 Cycle M 14.0000 8 0.00 +barcode1 14 -112 Cycle M 14.0000 11 1.00 +barcode1 14 -113 Cycle M 14.0000 9 0.00 +barcode1 14 -114 Cycle M 14.0000 11 0.00 +barcode1 14 -115 Cycle M 14.0000 8 0.00 +barcode1 14 -116 Cycle M 14.0000 9 0.00 +barcode1 14 -117 Cycle M 14.0000 9 0.00 +barcode1 14 -118 Cycle M 14.0000 4 0.00 +barcode1 14 -119 Cycle M 14.0000 9 1.00 +barcode1 14 -12 Cycle M 14.0000 7 0.00 +barcode1 14 -120 Cycle M 14.0000 7 0.00 +barcode1 14 -121 Cycle M 14.0000 9 0.00 +barcode1 14 -122 Cycle M 14.0000 12 0.00 +barcode1 14 -123 Cycle M 14.0000 5 0.00 +barcode1 14 -124 Cycle M 14.0000 5 0.00 +barcode1 14 -125 Cycle M 14.0000 9 0.00 +barcode1 14 -126 Cycle M 14.0000 4 0.00 +barcode1 14 -127 Cycle M 14.0000 4 0.00 +barcode1 14 -128 Cycle M 14.0000 6 0.00 +barcode1 14 -129 Cycle M 14.0000 6 0.00 +barcode1 14 -13 Cycle M 14.0000 3 0.00 +barcode1 14 -130 Cycle M 14.0000 2 0.00 +barcode1 14 -131 Cycle M 14.0000 10 0.00 +barcode1 14 -132 Cycle M 14.0000 9 0.00 +barcode1 14 -133 Cycle M 14.0000 5 0.00 +barcode1 14 -134 Cycle M 14.0000 6 0.00 +barcode1 14 -135 Cycle M 14.0000 8 0.00 +barcode1 14 -136 Cycle M 14.0000 7 0.00 +barcode1 14 -137 Cycle M 14.0000 2 0.00 +barcode1 14 -138 Cycle M 14.0000 8 0.00 +barcode1 14 -139 Cycle M 14.0000 4 0.00 +barcode1 14 -14 Cycle M 14.0000 1 0.00 +barcode1 14 -140 Cycle M 14.0000 8 1.00 +barcode1 14 -141 Cycle M 14.0000 4 0.00 +barcode1 14 -142 Cycle M 14.0000 8 0.00 +barcode1 14 -143 Cycle M 14.0000 8 0.00 +barcode1 14 -144 Cycle M 14.0000 6 0.00 +barcode1 14 -145 Cycle M 14.0000 8 1.00 +barcode1 14 -146 Cycle M 14.0000 3 0.00 +barcode1 14 -147 Cycle M 14.0000 3 0.00 +barcode1 14 -148 Cycle M 14.0000 7 0.00 +barcode1 14 -149 Cycle M 14.0000 13 2.00 +barcode1 14 -15 Cycle M 14.0000 5 0.00 +barcode1 14 -150 Cycle M 14.0000 3 0.00 +barcode1 14 -16 Cycle M 14.0000 4 0.00 +barcode1 14 -17 Cycle M 14.0000 4 0.00 +barcode1 14 -18 Cycle M 14.0000 3 0.00 +barcode1 14 -19 Cycle M 14.0000 7 0.00 +barcode1 14 -2 Cycle M 14.0000 4 0.00 +barcode1 14 -20 Cycle M 14.0000 3 0.00 +barcode1 14 -21 Cycle M 14.0000 4 0.00 +barcode1 14 -22 Cycle M 14.0000 3 0.00 +barcode1 14 -23 Cycle M 14.0000 3 0.00 +barcode1 14 -24 Cycle M 14.0000 7 1.00 +barcode1 14 -25 Cycle M 14.0000 6 0.00 +barcode1 14 -26 Cycle M 14.0000 5 0.00 +barcode1 14 -27 Cycle M 14.0000 2 0.00 +barcode1 14 -28 Cycle M 14.0000 6 0.00 +barcode1 14 -29 Cycle M 14.0000 3 0.00 +barcode1 14 -3 Cycle M 14.0000 4 0.00 +barcode1 14 -30 Cycle M 14.0000 4 0.00 +barcode1 14 -31 Cycle M 14.0000 5 0.00 +barcode1 14 -32 Cycle M 14.0000 6 0.00 +barcode1 14 -33 Cycle M 14.0000 6 1.00 +barcode1 14 -34 Cycle M 14.0000 5 0.00 +barcode1 14 -35 Cycle M 14.0000 4 0.00 +barcode1 14 -36 Cycle M 14.0000 6 1.00 +barcode1 14 -37 Cycle M 14.0000 7 0.00 +barcode1 14 -38 Cycle M 14.0000 3 0.00 +barcode1 14 -39 Cycle M 14.0000 4 0.00 +barcode1 14 -4 Cycle M 14.0000 6 0.00 +barcode1 14 -40 Cycle M 14.0000 4 0.00 +barcode1 14 -41 Cycle M 14.0000 7 0.00 +barcode1 14 -42 Cycle M 14.0000 4 0.00 +barcode1 14 -43 Cycle M 14.0000 9 0.00 +barcode1 14 -44 Cycle M 14.0000 4 0.00 +barcode1 14 -45 Cycle M 14.0000 5 1.00 +barcode1 14 -46 Cycle M 14.0000 8 1.00 +barcode1 14 -47 Cycle M 14.0000 4 0.00 +barcode1 14 -48 Cycle M 14.0000 5 0.00 +barcode1 14 -49 Cycle M 14.0000 6 0.00 +barcode1 14 -5 Cycle M 14.0000 2 0.00 +barcode1 14 -50 Cycle M 14.0000 4 0.00 +barcode1 14 -51 Cycle M 14.0000 5 0.00 +barcode1 14 -52 Cycle M 14.0000 7 1.00 +barcode1 14 -53 Cycle M 14.0000 8 0.00 +barcode1 14 -54 Cycle M 14.0000 2 0.00 +barcode1 14 -55 Cycle M 14.0000 3 0.00 +barcode1 14 -56 Cycle M 14.0000 7 0.00 +barcode1 14 -57 Cycle M 14.0000 6 0.00 +barcode1 14 -58 Cycle M 14.0000 5 0.00 +barcode1 14 -59 Cycle M 14.0000 6 0.00 +barcode1 14 -6 Cycle M 14.0000 3 0.00 +barcode1 14 -60 Cycle M 14.0000 8 0.00 +barcode1 14 -61 Cycle M 14.0000 6 0.00 +barcode1 14 -62 Cycle M 14.0000 7 0.00 +barcode1 14 -63 Cycle M 14.0000 4 1.00 +barcode1 14 -64 Cycle M 14.0000 7 1.00 +barcode1 14 -65 Cycle M 14.0000 13 0.00 +barcode1 14 -66 Cycle M 14.0000 5 0.00 +barcode1 14 -67 Cycle M 14.0000 5 0.00 +barcode1 14 -68 Cycle M 14.0000 6 1.00 +barcode1 14 -69 Cycle M 14.0000 7 0.00 +barcode1 14 -7 Cycle M 14.0000 4 0.00 +barcode1 14 -70 Cycle M 14.0000 6 0.00 +barcode1 14 -71 Cycle M 14.0000 9 0.00 +barcode1 14 -72 Cycle M 14.0000 12 1.00 +barcode1 14 -73 Cycle M 14.0000 6 1.00 +barcode1 14 -74 Cycle M 14.0000 7 0.00 +barcode1 14 -75 Cycle M 14.0000 2 0.00 +barcode1 14 -76 Cycle M 14.0000 6 2.00 +barcode1 14 -77 Cycle M 14.0000 7 0.00 +barcode1 14 -78 Cycle M 14.0000 8 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