https://sourceforge.net/p/denovocheck/home/Test/Recent changes to TestenThu, 14 Mar 2013 19:45:16 -0000https://sourceforge.net/p/denovocheck/home/Test/<div class="markdown_content"><pre>--- v27 +++ v28 @@ -3,10 +3,10 @@ The test files are simulated and purely intended to provide easy testing of the installation and see some of the features of the algorithm. -Data and files for testing DeNovoCheck are avaiable in the [Downloads](https://sourceforge.net/projects/denovocheck/files/) section. +Data and files for testing DeNovoCheck are available in the [Downloads](https://sourceforge.net/projects/denovocheck/files/) section. After extracting [DNC_testdata.tar.gz](http://sourceforge.net/projects/denovocheck/files/test/DNC_testdata.tar.gz/download) ./DNC_testdata/test.sh can be executed to test the program. -This file contains simulated bam files, a variant file and a precompiled (x86_64) version of samtools and the chr21 reference sequence (hg19). Please ensure propper execute rights have been set to prevent excecution failures. +This file contains simulated bam files, a variant file and a per-compiled (x86_64) version of samtools and the chr21 reference sequence (hg19). Please ensure proper execute rights have been set to prevent execution failures. The test.properties file can be adjusted to use for local variant and bam files, as described below. @@ -50,7 +50,7 @@ Setting up for a real run ================ -If the test.sh script finishes succesfully the software can be used to analyse your own data. +If the test.sh script finishes successfully the software can be used to analyze your own data. After opening test.properties file with a text editor the following lines should be adjusted: @@ -62,11 +62,17 @@ paternal_file=test/bam/father.bam # to the bam file of the father maternal_file=test/bam/mother.bam # to the bam file of the mother +samtools_directory=test/software/samtools/ reference_directory=test/reference/ # to the directory where the reference files are stored reference_format=chrX.fasta # according to the local reference format + +# Optional parameters, defaults specified here; +percentage_cutoff=2.0 +homozygous_cutoff=85.0 +min_vreads_cutoff=5 ~~~~~~ -This file should be stored in a new properties file, preferebly containing an identifier in the name, e.g. trio1.properties. +This file should be stored in a new properties file, preferably containing an identifier in the name, e.g. trio1.properties. This properties file should then be included in the command line argument like this: </pre> </div>Joep de LigtThu, 14 Mar 2013 19:45:16 -0000https://sourceforge.net818e6173efb1301f4da7c40bdcd0245354fd93efhttps://sourceforge.net/p/denovocheck/home/Test/<pre>--- v26 +++ v27 @@ -6,6 +6,8 @@ Data and files for testing DeNovoCheck are avaiable in the [Downloads](https://sourceforge.net/projects/denovocheck/files/) section. After extracting [DNC_testdata.tar.gz](http://sourceforge.net/projects/denovocheck/files/test/DNC_testdata.tar.gz/download) ./DNC_testdata/test.sh can be executed to test the program. +This file contains simulated bam files, a variant file and a precompiled (x86_64) version of samtools and the chr21 reference sequence (hg19). Please ensure propper execute rights have been set to prevent excecution failures. + The test.properties file can be adjusted to use for local variant and bam files, as described below. </pre>Joep de LigtFri, 28 Oct 2011 12:47:17 -0000https://sourceforge.net96970e44f429b27871c43ef2f9d0112bdc0ad464https://sourceforge.net/p/denovocheck/home/Test/<pre>--- v25 +++ v26 @@ -5,7 +5,7 @@ Data and files for testing DeNovoCheck are avaiable in the [Downloads](https://sourceforge.net/projects/denovocheck/files/) section. -After extracting DNC_testdata.tar.gz ./DNC/test.sh can be executed to test the program. +After extracting [DNC_testdata.tar.gz](http://sourceforge.net/projects/denovocheck/files/test/DNC_testdata.tar.gz/download) ./DNC_testdata/test.sh can be executed to test the program. The test.properties file can be adjusted to use for local variant and bam files, as described below. </pre>Joep de LigtFri, 28 Oct 2011 09:55:10 -0000https://sourceforge.net7aac0719a606bc9385d7798279a0ec8d1942c1c6https://sourceforge.net/p/denovocheck/home/Test/<pre></pre>Joep de LigtFri, 28 Oct 2011 09:30:39 -0000https://sourceforge.net1547c86c86fff3454924d2ab03fe6cf4a01cdd82https://sourceforge.net/p/denovocheck/home/Test/<pre>--- v23 +++ v24 @@ -5,7 +5,7 @@ Data and files for testing DeNovoCheck are avaiable in the [Downloads](https://sourceforge.net/projects/denovocheck/files/) section. -After extracting DNC_testdata.tar.gz ./DNC/test.sh can be executed to test the program, this packag contains a precompiled version of samtools, data files and a reference file. +After extracting DNC_testdata.tar.gz ./DNC/test.sh can be executed to test the program. The test.properties file can be adjusted to use for local variant and bam files, as described below. </pre>Joep de LigtFri, 28 Oct 2011 09:10:00 -0000https://sourceforge.net4898ce30dd8bdd14f30e9fa0b6907ad7dedf8985https://sourceforge.net/p/denovocheck/home/Test/<pre>--- v22 +++ v23 @@ -39,6 +39,9 @@ Chromosome Start position End position reference mutation reads variation reads % variation Abberation ID QUAL FILTER INFO FORMAT child.bam DNC_Inherited DNC_InheritanceType DNC_Comments INDEX|%Variation PATERNAL|%Variation MATERNAL|%Variation INDEX INDEX|A C G T N + - * INDEX|+Ref +Var -Ref -Var INDEX|Quality INDEX|Calls PATERNAL PATERNAL|A C G T N + - * PATERNAL|+Ref +Var -Ref -Var PATERNAL|Quality PATERNAL|Calls MATERNAL MATERNAL|A C G T N + - * MATERNAL|+Ref +Var -Ref -Var MATERNAL|Quality MATERNAL|Calls chr21 33057757 33057757 T A 29 13 44.827586206896555 substitution . 135.0 . DP=30;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,13;MQ=59;FQ=138;PV4=1,0.49,0.27,0.37 GT:PL:GQ 0/1:165,0,178:99 Yes PATERNAL 0.43333333333333335 0.4 0.0 INDEX|chr21:33057757 (T) A (17) 13 13 0 0 17 0 0 0 0 0 0 17 13 40 40 40 40 40 40 39 40 40 40 40 38 40 40 40 40 40 38 40 6 40 40 40 40 40 25 40 40 40 23 T a T a T a T T a T a T a T a T T T a T a T T a a T T a T a PATERNAL|chr21:33057757 (T) A (18) 12 12 0 0 18 0 0 0 0 0 0 18 12 40 40 40 40 40 40 39 40 40 40 40 38 40 40 40 40 40 38 40 6 40 40 40 40 40 25 40 40 40 23 T T T a T a T T a T a T T a a a T T a T a T T a T T T a T a MATERNAL|chr21:33057757 (T) T (30) 30 0 0 0 30 0 0 0 0 0 0 30 0 40 40 40 40 40 40 39 40 40 40 40 38 40 40 40 40 40 38 40 6 40 40 40 40 40 25 40 40 40 40 T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T chr21 33057765 33057765 T G 31 30 96.7741935483871 substitution . 75.0 . DP=33;AF1=1;CI95=1,1;DP4=0,1,0,30;MQ=59;FQ=-89;PV4=1,0.056,0.41,1 GT:PL:GQ 1/1:108,62,0:99 Yes OTHER NON_MENDELIAN, 0.9696969696969697 0.5151515151515151 0.0 INDEX|chr21:33057765 (T) G (1) 32 0 0 32 1 0 0 0 0 0 0 1 32 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 4 17 17 17 17 17 17 17 17 17 17 17 17 17 17 31 0 g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g T g PATERNAL|chr21:33057765 (T) G (16) 17 0 0 17 16 0 0 0 0 0 0 16 17 40 17 17 40 17 40 40 17 40 17 40 17 40 17 17 40 4 40 17 40 17 40 17 40 17 40 17 40 40 17 17 26 26 T g g T g T T g T g T g T g g T g T g T g T g T g T g T T g g g T MATERNAL|chr21:33057765 (T) T (33) 33 0 0 0 33 0 0 0 0 0 0 33 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 40 40 40 40 40 40 40 40 40 40 40 40 31 26 T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T +chr21 33057771 33057771 G T 35 18 51.42857142857142 substitution . 75.0 . DP=35;AF1=0.5;CI95=0.5,0.5;DP4=0,17,0,18;MQ=59;FQ=78;PV4=1,1.2e-08,0.4,0.35 GT:PL:GQ 0/1:105,0,174:99 Yes MATERNAL 0.5142857142857142 0.0 0.9714285714285714 INDEX|chr21:33057771 (G) T (17) 18 0 0 17 18 0 0 0 0 0 0 17 18 40 22 40 22 22 40 22 40 40 31 40 22 40 22 31 22 15 40 22 29 40 22 40 22 22 40 22 38 22 40 24 40 22 40 26 G t G t t G t G G t G t G t G t G G t t G t G t t G t G t G t G t G t PATERNAL|chr21:33057771 (G) G (35) 35 0 0 35 0 0 0 0 0 0 0 35 0 40 40 40 40 40 40 40 40 40 31 40 40 40 40 31 40 15 40 40 33 40 40 40 40 40 40 40 38 40 40 38 40 40 40 26 G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G MATERNAL|chr21:33057771 (G) T (1) 34 0 0 1 34 0 0 0 0 0 0 1 34 22 22 22 22 22 22 22 22 22 31 22 22 22 22 31 22 15 22 22 29 22 22 40 22 22 22 22 24 22 22 24 22 22 22 26 t t t t t t t t t t t t t t t t t t t t t t G t t t t t t t t t t t t +chr21 33057778 33057778 G C 36 35 97.22222222222221 substitution . 85.0 . DP=36;AF1=1;CI95=1,1;DP4=0,1,0,35;MQ=58;FQ=-120;PV4=1,0.39,1,1 GT:PL:GQ 1/1:118,93,0:99 Yes SHARED 0.9722222222222222 0.5 0.4444444444444444 INDEX|chr21:33057778 (G) C (1) 35 0 35 1 0 0 0 0 0 0 0 1 35 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 13 16 16 16 16 16 16 16 20 c c c c c c c c c c c c c c c c c c c c c c c c c c c c c c c c c c c G PATERNAL|chr21:33057778 (G) C (18) 18 0 18 18 0 0 0 0 0 0 0 18 18 40 16 16 40 16 40 16 40 16 16 16 40 16 40 16 40 16 40 16 40 16 16 40 40 16 40 16 40 16 40 16 40 16 40 16 20 G c c G c G c G c G c G c G c G c G c G c c G G c G c G c G c G c G c G MATERNAL|chr21:33057778 (G) C (20) 16 0 16 20 0 0 0 0 0 0 0 20 16 40 16 16 16 40 40 16 40 16 16 40 40 16 40 16 40 16 40 40 16 16 40 16 40 16 40 40 13 40 16 40 16 40 16 40 20 G c c c G G c G c G G G c G c G c G G c c G c G c G G c G c G c G c G G +chr21 33057787 33057787 A C 33 12 36.36363636363637 substitution . 144.0 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=0,21,1,11;MQ=59;FQ=147;PV4=0.36,1,0.038,1 GT:PL:GQ 0/1:174,0,183:99 No POSSIBLE de novo 0.42105263157894735 0.0 0.0 INDEX|chr21:33057787 (A) C (22) 16 22 16 0 0 0 0 0 0 0 1 22 15 36 0 36 6 40 40 40 35 40 40 40 35 27 40 40 40 40 37 40 40 40 40 40 40 40 4 40 40 40 24 4 40 40 7 40 40 40 40 A c A c A A A c A c A c A c A A c c A A c A c A A A c c A A c A A c c A C A PATERNAL|chr21:33057787 (A) A (38) 38 38 0 0 0 0 0 0 0 1 0 37 0 36 36 36 40 40 40 40 39 40 40 40 35 27 40 40 40 40 37 40 40 40 40 40 40 40 4 40 40 40 24 4 40 40 7 40 40 40 40 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A MATERNAL|chr21:33057787 (A) A (38) 38 38 0 0 0 0 0 0 0 1 0 37 0 36 36 36 40 40 40 40 39 40 40 40 35 27 40 40 40 40 37 40 40 40 40 40 40 40 4 40 40 40 24 4 40 40 7 40 40 40 40 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A ~~~~~~ ---------------- </pre>Joep de LigtThu, 27 Oct 2011 16:22:10 -0000https://sourceforge.net6554d64f1b11d26a23f0805b2581bed8b92674d5https://sourceforge.net/p/denovocheck/home/Test/<pre>--- v21 +++ v22 @@ -34,6 +34,7 @@ ================ The output of the test case should be as follows: + ~~~~~~ Chromosome Start position End position reference mutation reads variation reads % variation Abberation ID QUAL FILTER INFO FORMAT child.bam DNC_Inherited DNC_InheritanceType DNC_Comments INDEX|%Variation PATERNAL|%Variation MATERNAL|%Variation INDEX INDEX|A C G T N + - * INDEX|+Ref +Var -Ref -Var INDEX|Quality INDEX|Calls PATERNAL PATERNAL|A C G T N + - * PATERNAL|+Ref +Var -Ref -Var PATERNAL|Quality PATERNAL|Calls MATERNAL MATERNAL|A C G T N + - * MATERNAL|+Ref +Var -Ref -Var MATERNAL|Quality MATERNAL|Calls chr21 33057757 33057757 T A 29 13 44.827586206896555 substitution . 135.0 . DP=30;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,13;MQ=59;FQ=138;PV4=1,0.49,0.27,0.37 GT:PL:GQ 0/1:165,0,178:99 Yes PATERNAL 0.43333333333333335 0.4 0.0 INDEX|chr21:33057757 (T) A (17) 13 13 0 0 17 0 0 0 0 0 0 17 13 40 40 40 40 40 40 39 40 40 40 40 38 40 40 40 40 40 38 40 6 40 40 40 40 40 25 40 40 40 23 T a T a T a T T a T a T a T a T T T a T a T T a a T T a T a PATERNAL|chr21:33057757 (T) A (18) 12 12 0 0 18 0 0 0 0 0 0 18 12 40 40 40 40 40 40 39 40 40 40 40 38 40 40 40 40 40 38 40 6 40 40 40 40 40 25 40 40 40 23 T T T a T a T T a T a T T a a a T T a T a T T a T T T a T a MATERNAL|chr21:33057757 (T) T (30) 30 0 0 0 30 0 0 0 0 0 0 30 0 40 40 40 40 40 40 39 40 40 40 40 38 40 40 40 40 40 38 40 6 40 40 40 40 40 25 40 40 40 40 T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T </pre>Joep de LigtThu, 27 Oct 2011 16:20:41 -0000https://sourceforge.net9b58fff98b948da71a33546b7d608e86d24d6231https://sourceforge.net/p/denovocheck/home/Test/<pre>--- v20 +++ v21 @@ -11,21 +11,34 @@ ---------------- -Test data -================ - +Test data input +================ + A screenshot of the data stored in the bam files is available in DNC_testdata.jpg, in the attachment. The variants are simulated to illustrate the following inheritance patterns: Position | Child | Father | Mother | DNC Inherited | DNC InheritanceType | DNC Comments -------- | -- | -- | -- | -- | -- | -- 33057757 | TA | TA | TT | Yes | Paternal | 33057765 | GG | TG | TT | Yes | Other | NON_MENDELIAN 33057771 | GT | GG | TT | Yes | Maternal | 33057778 | CC | GC | GC | Yes | Shared | 33057787 | AC | AA | AA | No | POSSIBLE *de novo* | * Positions and genotypes are generated on the hg19 ([GRCh37](http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml)) reference genome. + +---------------- + + +Test data output +================ + +The output of the test case should be as follows: +~~~~~~ +Chromosome Start position End position reference mutation reads variation reads % variation Abberation ID QUAL FILTER INFO FORMAT child.bam DNC_Inherited DNC_InheritanceType DNC_Comments INDEX|%Variation PATERNAL|%Variation MATERNAL|%Variation INDEX INDEX|A C G T N + - * INDEX|+Ref +Var -Ref -Var INDEX|Quality INDEX|Calls PATERNAL PATERNAL|A C G T N + - * PATERNAL|+Ref +Var -Ref -Var PATERNAL|Quality PATERNAL|Calls MATERNAL MATERNAL|A C G T N + - * MATERNAL|+Ref +Var -Ref -Var MATERNAL|Quality MATERNAL|Calls +chr21 33057757 33057757 T A 29 13 44.827586206896555 substitution . 135.0 . DP=30;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,13;MQ=59;FQ=138;PV4=1,0.49,0.27,0.37 GT:PL:GQ 0/1:165,0,178:99 Yes PATERNAL 0.43333333333333335 0.4 0.0 INDEX|chr21:33057757 (T) A (17) 13 13 0 0 17 0 0 0 0 0 0 17 13 40 40 40 40 40 40 39 40 40 40 40 38 40 40 40 40 40 38 40 6 40 40 40 40 40 25 40 40 40 23 T a T a T a T T a T a T a T a T T T a T a T T a a T T a T a PATERNAL|chr21:33057757 (T) A (18) 12 12 0 0 18 0 0 0 0 0 0 18 12 40 40 40 40 40 40 39 40 40 40 40 38 40 40 40 40 40 38 40 6 40 40 40 40 40 25 40 40 40 23 T T T a T a T T a T a T T a a a T T a T a T T a T T T a T a MATERNAL|chr21:33057757 (T) T (30) 30 0 0 0 30 0 0 0 0 0 0 30 0 40 40 40 40 40 40 39 40 40 40 40 38 40 40 40 40 40 38 40 6 40 40 40 40 40 25 40 40 40 40 T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T +chr21 33057765 33057765 T G 31 30 96.7741935483871 substitution . 75.0 . DP=33;AF1=1;CI95=1,1;DP4=0,1,0,30;MQ=59;FQ=-89;PV4=1,0.056,0.41,1 GT:PL:GQ 1/1:108,62,0:99 Yes OTHER NON_MENDELIAN, 0.9696969696969697 0.5151515151515151 0.0 INDEX|chr21:33057765 (T) G (1) 32 0 0 32 1 0 0 0 0 0 0 1 32 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 4 17 17 17 17 17 17 17 17 17 17 17 17 17 17 31 0 g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g T g PATERNAL|chr21:33057765 (T) G (16) 17 0 0 17 16 0 0 0 0 0 0 16 17 40 17 17 40 17 40 40 17 40 17 40 17 40 17 17 40 4 40 17 40 17 40 17 40 17 40 17 40 40 17 17 26 26 T g g T g T T g T g T g T g g T g T g T g T g T g T g T T g g g T MATERNAL|chr21:33057765 (T) T (33) 33 0 0 0 33 0 0 0 0 0 0 33 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 40 40 40 40 40 40 40 40 40 40 40 40 31 26 T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T +~~~~~~ ---------------- </pre>Joep de LigtThu, 27 Oct 2011 16:20:19 -0000https://sourceforge.netc9f586463e81183457c97b6c284f4e281499f018https://sourceforge.net/p/denovocheck/home/Test/<pre>--- v19 +++ v20 @@ -5,7 +5,7 @@ Data and files for testing DeNovoCheck are avaiable in the [Downloads](https://sourceforge.net/projects/denovocheck/files/) section. -After extracting DNC_testdata.tar.gz ./test.sh can be executed to test the program, this packag contains a precompiled version of samtools, data files and a reference file. +After extracting DNC_testdata.tar.gz ./DNC/test.sh can be executed to test the program, this packag contains a precompiled version of samtools, data files and a reference file. The test.properties file can be adjusted to use for local variant and bam files, as described below. </pre>Joep de LigtThu, 27 Oct 2011 16:06:30 -0000https://sourceforge.net8f2e759a31a27445906ad9e25364d96e10e5fdd2https://sourceforge.net/p/denovocheck/home/Test/<pre>--- v18 +++ v19 @@ -55,6 +55,11 @@ java -Xms500m -Xmx500m -jar test/software/DeNovoCheck/DeNovoCheck.jar -properties trio1.properties ~~~~~~ +When using command line options rather the a properties file the following call can be made: + +~~~~~~ +java -Xms500m -Xmx500m -jar test/software/DeNovoCheck/DeNovoCheck.jar -mutation_file test/child.vcf -output_file test/child.dnc.txt -index_file test/bam/child.bam -paternal_file test/bam/father.bam -maternal_file test/bam/mother.bam -samtools_directory test/software/samtools/ -reference_directory test/reference/ -reference_format chrX.fasta +~~~~~~ ---------------- </pre>Joep de LigtThu, 27 Oct 2011 15:53:43 -0000https://sourceforge.nete1086027e282300d850635890b2bd07d9ceff233