DeNovoCheck Home
DeNovoCheck: Inheritance analysis for NGS trio data
Brought to you by:
denovocheck,
joepdl
Test
Test files and procedures
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 available in the Downloads section.
After extracting DNC_testdata.tar.gz (sourceforge.net) ./DNC_testdata/test.sh can be executed to test the program.
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.
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) 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
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
Setting up for a real run
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:
mutation_file=test/child.vcf # to a variant file of interest
output_file=test/child.dnc.txt # to a file in which to store the results
index_file=test/bam/child.bam # to the bam file of the child
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, 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:
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
Related
