NovoWorx User Manual V1.0- Exome Workflow
Contents
1. f Jobs View information regarding the jobs that are currently running 2015 Novocraft Technologies www novocraft com 15 4 0 The Job Status Panel The Job Status Panel shows the list of jobs completed or currently running for a particular project Double clicking on the job will bring up a splash panel with the details of the modules that have been run to completion as well as the queued and running jobs O Create is Refresh List View All OutputFiles w 4 Start Wizard Options Help kaanesh kaanesh novocraft con NOVOCRAF Module Sample Name Module Status Date Started Date Last Updated Elapsed Time Muktizample Exome Ver 1 01 Mapping Novoalign_V3 02 12 test normal sa FINISHED 2015 09 09 16 1 2015 08 08 18 3 03 13 06 Mukizample Exome Ver 1 01 Merging Novosort_v1 03 03 test normal sa FINISHED 2015 09 09 19 3 2015 09 09 18 3 00 06 13 Multizample Exome Ver 1 01 test normal sa FINISHED 2015 09 09 18 3 2015 09 09 19 3 00 00 56 Multizample Exome Ver 101 Variants Calling Samtools v1 2 test normal sa FINISHED 2015 09 09 18 3 2015 09 09 20 0 00 28 41 Mulkizample Exome Wer 101 Variants Annotation test normal ga FINISHED 2015 09 09 20 0 2015 09 09 20 3 00 26 55 Mutizample Exome Ver 101 Base Coverage Analysis test normal ga FUNNING 2015 09 09 20 3 0000 00 00 00 0 00 00 00 5 0 Viewing2. 9 0b linux AMD64 set 054 gcat set 054 bed gcat set 054 lfastq uA GeneTorrent 3 8 7 9 gtkdialog 0 8 3 Click and drag the empty space next to the file name and drop it in the file location field Do the same with the second file for paired end data Click on Save Project to continue 2015 Novocraft Technologies www novocraft com 12 Step 6 Project Information Project Name test Project Description test novoalign Reference HG19 new order Workflow Name 2015 Human Exome Analysis version Workflow Description Pipeline for Reads mapping and alignment duplicate marking variants calling and annotation and coverage analysis Input is Fastq or fastq gz and bedfile C g Reload Panel Run Project See Published Links Edit Once you click on Save Project the job creation splash panel will close and the Project information splash panel will open with a dialogue box confirming the creation of the project Click OK and then click on Run Project to start running your project 2015 Novocraft Technologies www novocraft com 13 Step 7 plash Pane Project test Job Contig Workflow Global Options Select Notification Level Do Not Send Any Emails a Multisample Exome Ver 1 01 Mapping Novoalign_V3 02 12 options Parameters Enable quality calibration 2 3V Adapter to Strip m Truncate reads to specified length a Multisample Exome Ver LOL Base Coverage A
3. and Monitoring your results The results of the pipeline are grouped by the modules that have been run within the pipeline Each module will have 3 sub folders which are Inputs Pipeline Results and Summarized Reports Each of these sub folders has one sub folder for each sample used in the module Within each sample sub folder is the output files for each of the modules which can be viewed in the novoWorx interface The Inputs sub folder has a list of the input files that have been used in the pipeline The Pipeline Results sub folder has the list of pipeline outputs for each module detailed Description of the type of files and the views for each file is detailed in the Output Files Section The Summary Reports folder contains a summarized report for the entire pipeline that is compiled after conclusion Not all of the pipelines have a summarized report and the folder may therefore be empty There are a few methods of viewing your results in the novoWorx user interface 2015 Novocraft Technologies www novocraft com 16 6 0 Using the sidebar 3 e test a Inputs a Pipeline Fesuls Alignment 3j A Mukisample Exome Ver 1 01 Merging Hovosort v 1 03 0 af test normal samplel sip test normal sample 1 3 A Exome Ver 1 01 Mapping Novoalign_V3 02 Mf ocat_set_053 1 fastq as 14947 unsorted bam as 14947 novoalignintoTable html a 14947 indels tawv Coverage Anal
4. lst fragments 1000 last fragments 1000 freads mapped 1991 reads mapped and paired 1984 reads unmapped 9 reads properly paired 1984 reads paired 2000 freads duplicated 0 reads 0 reads QC failed 0 Inon primary alignments 0 otal length 302000 ases mapped 300641 bases mapped cigar 240510 bases trimmed 0 bases duplicated 0 mismatches 2484 lerror rate 1 032805e 02 laverage length 151 maximum length 151 average quality 35 1 insert size average 132 3 insert size standard deviation 9 2 inward oriented pairs 466 outward onented pairs 0 pairs with other orientation 0 pars on different chromosomes 0 2015 Novocraft Technologies www novocraft com 25
5. the drop down menu Different workflows have different uses Make sure you select the right one Once this is done click Next 2015 Novocraft Technologies www novocraft com Step 3 wv 4989 Create Start Wizard Options Help Project Name test Project test novoalign Description Reference HG19 new order Here you can input the name and description for the project as well as select a suitable reference to use Click Next to continue Step 4 v Create Start Wizard Options Help Upload Via Add 10 More Condition ResetForm New Condition 1 Add A Sample Remove Condition Once the splash panel comes up enter a condition name before clicking on Add a Sample The condition name is not unique and samples with the same condition will be merged together This will mean that the samples with the same condition name will be merged into a single vcf file If this is not desirable for your research please separate the samples and provide unique names for each condition for example Tumor 1 Tumor 2 etc 2015 Novocraft Technologies www novocraft com 10 Step 5 Once the sample is named the File Compression must be selected If no compression is used select None The file format is dependent on the sequencing technology in use at your facility NovoWorx currently supports FASTA and FASTQ of both Illumina and ABI SOLID Colorspace reads 4 New Condition 1 Condition N
6. 0 1 42 0 197 0 1 42 0 191 0 1 54 0 54 0 1 45 0 141 0 1 45 0 163 0 1 39 0 218 0 1 39 0 217 0 1 39 0 218 0 1 39 0 218 0 1 48 0 140 0 1 48 0 140 JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse View in JBrowse In novoWorx the VCF format is made easy to read by splitting the tabs into columns that can be sorted The VCF file is also viewable in Jbrowse to show the location of the variant in the aligned BAM file Clicking on the button opens the Jbrowse tab and jumps to the location of the variant 2015 Novocraft Technologies www novocraft com 22 8 3 CSV amp TSV amp BED A CSV file is a file where the separator between fields is a comma and a TSV file is a file where the separator between fields is a tab A BED file is a tab separated file that is generally comprised of a list of genomic range NovoWorx separates each field into an easy to view format NovoWorx also makes searching for values easier using the Filter function by specifying the fields as shown below Filter rgl dpFilter tsv 4 Choose Columns Column Select a Column v Type Se
7. File O Download File export home app_user framework files WORKSPACE 193 818 1 13346 exomeModuleLog test normal samplel tsv FINISHED view File Download File lexport home app user framework files WORKSP ACE 193 818 1 13346 exomeNovosort_ test normal samplel bai FINISHED view File O Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeNovosort test normal samplel txt FINISHED View File O Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeModuleLog test normal samplel tsv FINISHED view File O Download File Clicking on View File will open the file in the novoWorx interface Take note that not all files formats are supported by novoWorx For a list of files that are supported please navigate to the Output Files Section of this manual Files may also be downloaded for viewing outside of the novoWorx platform by clicking on the Download File button A description of the files available is included in the Output Files Section 2015 Novocraft Technologies www novocraft com 19 8 0 Output Files NovoWorx is able to handle most standard bioinformatics file formats and is able to display them in an easy to process manner Among the file formats supported by novoWorx are BAM The following sections of this manual show examples of how the files are displayed in novoWorx 2015 Novocraft Technologies www novocraft com 8 1 BAM A BAM file is a
8. Grid 13721 8181 2015 09 09 16 1 Workflow Name Multisample 2015 Human Exome Analysis version 1 01 Workflow Description Pipeline for Reads mapping and alignment duplicate marking variants calling and annotation and coverage analysis Input is Fastq or fastq gz KillLast Job Reload Panel Condition Information Add Condition Condition ID Condition Name Date Created 10004 test_normal 2015 09 09 16 10 28 Sequence File Name 1 Sequence File Name 2 Sequence Description DTE gcat set 053 2 fastq em a C See Published Links Edit Job End Status Process ID Job Not Completed 5537 Job ID Project ID Job Start Job Complete Job Current Status Module exomeNovoalign has started 6 outputs detected 7 Legend Option Description 1 Kill Last Job Kill the most recent running job for the selected project 2 Reload Panel Reload the job status panel and update the running module as well as the job status 3 Published Links Open a splash panel that shows the list of downloadable files in the form of web links that can be downloaded via FTP 4 Edit Allows the user to edit the project name and description 5 Condition View details regarding the conditions already available and add conditions as Information the project is running 6 Sequence View the information regarding the sequence sets for each of your Information conditions
9. NOVOCRAFI TECHNOLOGIES SDN BHD NovoWorx User Manual Version 1 0 EXOME WORKFLOW Table of Contents 2015 Novocraft Technologies www novocraft com 2 1 0 Using the Multisample CSV file input The exome multisample project workflow is designed to enable users to design and run a large set of data samples without having to input each sample individually This is done using a comma separated value file which holds all the necessary information to set up the experiment To create a Workflow the csv file has to be populated with the following details sample name condition format type filel file2 mean stddev sample name The individual sample name This is a unique identifier for each sample condition The sample condition All samples with the same condition will be merged and will produce one BAM and one VCF per condition format The fomat of the file This is either fastq csfastq fasta or csfasta type The type of read This is either Mate Pair Pair End or Fragment file2 optional The full path of the second read This may be left blank if only one read is present mean optional The mean of the read length in base pairs This field is optional and may be left empty stddev optional The Standard Deviation of the read length in base pairs This field is optional and may be left empty 2015 Novocraft Technologies www novocraft com 3 An example of a line in the CSV file is as below Example of
10. a sample with 2 reads NFLE 6417 fastq paired end nome user 6417_R1 fastq gz nome user 6417_R2 fastq gz 0 0 Example of a sample with only 1 read including the mean and standard deviation NFLE 6417 fastq paired end home user 6417 R1 fastq gz 0 0 Example of a sample with only 1 read and NOT inclusive of the mean and standard deviation NFLE 6417 fastq paired end home user 6417 R1 fastq gz Each line represents one sample in the experiment It should be noted that the novoWorx pipeline groups all the samples into the condition that they are placed in If separate BAM files are necessary they should be named uniquely as follows NFLE 6417 6417 fastq paired end home user 6417 R1 fastq gz home user 6417 R2 fastq gz 0 0 NFLE 6418 6418 fastq paired end home user 6417 R1 fastq gz home user 6417 R2 fastq g9z 0 0 2015 Novocraft Technologies www novocraft com 2 0 Starting your workflow 2 1 Creating your Project Step 1 wv Create Start Wizard Options Help e a Create Reference it Create Workflow Create Module add Mounted Drive A create User da Create Group Start Wizard Create New Project View Jobs When logged on to novoWorx click on the Create button and select Create Project 2015 Novocraft Technologies www novocraft com Step 2 Splash Panel Project Add New Project Name test Project Description test multisample Workflow Multisample 2015 Human Exome Analysis v
11. ame test normal Add New Sample Sample test normal samplel Sample Description Optional File Compression None none ow File Format fast lumina Add Sequence File 0 Library Type Paired End X Mean Optional standard Deviation Optional sequence File Hame Optional sequence File Description Optional File 1 Location File 2 Location Remove Sequence File Select the Library type whether single ended or paired end reads and the other optional reads may be left blank if no custom value is desired for the fields To input the read file location one can key in the location of the file or the file can be dragged and dropped from the mounted drives as shown in the following images My Mounted Drives LARS E My Users LAI S E My Groups LATIO A My References Elm E My Workflows Elm E My Modules Elm E Help Menu E 2015 Novocraft Technologies www novocraft com 11 Click on My Mounted Drives to get an expandable list of drives and files mounted and navigate to the location of the desired file a akzam app user ula ben ua colin deepam J3 kaamesh a BE Aligner Android Aa AndroidstudioProjects 3 af 1 9 cmake 2 8 112 Desktop a Documents a Downloads 011 Bl android sdk linux bcftools 1 2 la cahub 2 dai cghub al cahub genetorrent 476d7bd44985 ua crystalxtheme ula freebayes a irizing O
12. compressed file format that contains the alignments in a binary format Further information regarding the BAM and SAM formatting can be obtained at the SAMTOOLS format specification page Double Clicking on the BAM file within the novoWorx interface will bring up the Jbrowse Genome Browser as shown in the image below Available Tracks 40 000 000 60 000 000 100 000 000 O Q ec chri1 chr11 80973582 80973637 57 b Gol 80 973 600 80 973 625 120 000 000 20 000 000 test normal samplel bam alignment test normal samplel bam snpcoverage test normal samplei bam alignment HG19 DBSNP 132 HG19 Known Genes HG19 MirBase HSA HG19 RefSeq Genes Reference sequence Reference sequence test normal samplel ann vcf HG19 RefSeq Genes test normal samplel var vcf HG19 MirBase HSA HG19 Known Genes HG19 DBSNP 132 Here the BAM file can be viewed in tandem with the reference files The BAM file is also downloadable for viewing in the Broad Institute Integrative Genomics Viewer IGV To download the BAM file navigate to the Alignment section on the sidebar and click the sample file to view the aligned BAM file Right click on the BAM file and select Download from the list of options You can also download the file by navigating the Job Information panel 2015 Novocraft Technologies www novocraft com 21 8 2 VCF The VCF format is the standard format tha
13. ers v Reference HG19 new order n Multisample Options None Local Server File gt Local Server File Please Drag and drop or Paste the file path Example path to file file_l csv Direct Upload e Direct Upload Max Size 20 MB CMakepathiMultisample config csv Browse lt File should be in this form at Sample Name Condition Format Type File1 File2 if any Mean Std Deviation Example 1 sample 1 condition 1 fastq fragment patlVto file file 1 fastq Example 2 sample 2 condition 2 fastq mate pair patlto file file 1 fastq patlvto file file 2 fastq 1 2 Fill in the details of the project as desired Click on the Direct Upload radio button and browse for the CSV configuration file o 24 mim mit Cancel Once the CSV file is uploaded click on the Save button at the bottom of the page Click OK on the project creation confirmation dialog pop up Step 3 2015 Novocraft Technologies www novocraft com 6 a Today s test EE Yesterday On the side bar you will see the project that you have just created Click on the name of the project and the splash panel will open a tab detailing the project information O lC eo S9 og Kili asi Job Reload Panel Run Project See Published Links Edit Click on Run Project and you will proceed to the final step of the process 2015 Novocraft Technologies www novocraft com T Step 4 Workflow Global Options Select Noti
14. fication Level Do Hot Send Any Emails Multisample Exome Ver 1 01 Mapping Hovoalign V3 02 12 options 4 Parameters Enable quality calibration 3 Adapter to Strip Truncate reads to specified length Multisample Exome Ver 1 01 Base Coverage Analysis options a Parameters BedFile Submit Cancel If you desire to use any additional options you may do so in the final splash panel Once all the desired options are selected click the Submit button A notification will pop up with the Job ID confirming that the job has been started 2015 Novocraft Technologies www novocraft com 2 2 Using the novoWorx job creation wizard Step 1 wv 4989 Create Start Wizard Options Help Splash Panel d yir e E Start Wizard Create New Project View Jobs Click on the Start Wizard Button Step 2 wv L Create Start Wizard Options Help Splash Panel Create Project Wizard STEP 1 Choose A Workflow STEP2 CreateProject STEP 3 Add Conditions Workflow v Basic Novoalign Workflow FastQC novoindex exp Human Genome Analysis Samtools Variant Breakdancer bam input testStructural Variation Detection Breakdanc SV detect Structural Variation Detection Breakdancer Pindel SV BAM 2014 Basic Human Exome Analysis unused Pindel SV annotation Ensembl SV Annotation Breakdancer SV Annotation Ensembl SV AnnotationVCF 2015 Human Exome Analysis version 1 01 Select a Workflow from
15. job that has been run Double clicking on the Job ID that you wish to view will bring up a list of the completed modules or running modules as shown below _ BI LR kaanesh i NO vo CRI kaanesh novocraft con Create Start Wizard Options Help plash Panel Project test 3 Project test 1 C Refresh List View All Output Files Module Mame Sample Mame Module Status Date Started Date Last Updated Elapsed Time Multizample Exome Ver 1 01 Mapping Hovoalign V 3 02 12 test normal sa FIMISHED 2015 09 09 16 1 2015 09 09 19 3 03 13 06 Multizample Exome Ver 1 01 Merging Novosort_v1 03 03 test normal sa FINISHED 2015 09 09 19 3 2015 09 09 19 3 00 06 13 IMultisample Ver 1 01 test normal sa FINISHED 2015 09 09 15 3 2015 09 09 19 3 00 00 56 Multizample Exome Ver 101 Variants Calling Samtools v1 2 test normal sa FINISHED 2015 09 09 19 3 2015 09 09 20 0 00 28 41 Exome Ver 1 01 Variants Annotation test normal sa FINISHED 2015 09 09 20 0 2015 09 09 20 3 00 26 55 Idultisample Exome Ver 101 Base Coverage Analysis test normal sa FINISHED 2015 09 09 20 3 2015 09 10 10 3 13 59 42 Based the image above 1 Clicking on the results you would like to view will bring up a list of associated documents and or files that can be viewed in novoWorx or downloaded for your reference a
16. lect Type v Add Filter Criteria 2015 Novocraft Technologies www novocraft com 23 8 4 HTML As novoWorx is a browse based interface HTML files will be opened in a new Browser tab and can be viewed in the native HTML format MODULE ATTRIBUTES Novoalign version Licenced To Input Type Input Format Input Files Interpretation Input Files Name Commands Index Build Version Hash Length Step Size Paired Reads Proper Pairs Read Sequences Unique Alignment Multi Mapped Novoalign Report 14947 y3 02 12 Build Feb 13 2015 12 41 35 Movocraft Technologies Sdn Bhd Internal Use Only Paired End fastg Illumina FASTQ Casava Pipeline 1 8 amp later gcat set O53 1 gcat set 053 2 fastq hlimt 8 p 5 20 softclip 20 d HG19 new order idx 14947 mismatch tsv 0 SAM hpstats 14947 indels tsv H 20 E 16 t 20 4 f gcat set O53 l fastq gcat set 053 2 fastq 3 0 14 2 45038905 44430521 90077810 79289074 10035642 98 6 88 0 11 1 2015 Novocraft Technologies www novocraft com 24 8 5 TXT The TXT format is a basic non formatted text file In novoWorx the txt files are displayed in a standard tab with no formatting and will look like you opened the file with any standard text editor NovoWorx does NOT allow editing for text files total sequences 2000 filtered sequences 0 sequences 2000 hs sorted 1
17. nalysis options a Parameters BedFile Submit The final splash panel is where you input the final options for the project If none of these options are desired or you would prefer the default values leave them blank and click Submit You will get another dialog box letting you know that the job has been submitted and the job is now running Project Information Project Name Project Description Reference Workflow Name Workflow Description test test novoalign HG19 new order Multisample 2015 Human Exome Analysis version 1 01 Pipeline for Reads mapping and alignment duplicate marking variants calling and annotation and coverage analysis Input is Fastq or fastq gz and bedfile e Cc KillLastJob Reload Panel See Published Links Edit 2015 Novocraft Technologies www novocraft com 14 3 0 Navigating a Running Project When logged on to novoWorx clicking on the project name will bring up the project information splash panel From here multiple options such as viewing jobs updating jobs or view output files are accessible as described below m ow w k h fe T T 4 kaaneshenovocraft con 4 A1 NO VO C RA FI Create Download Files Delete Edit Sharing Start Wizard Options Help Project Information Project Name test test novoalign HG19 new order Project Description Reference and bedfile C Refresh Job
18. rAnnota test normal samplel FINISHED View File O Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeVarAnnota test normal samplel tsv FINISHED View File Download File lexport home app user framework files WORKSP ACE 193 8 18 1 13346 exome Var Annota test normal samplel html FINISHED view File O Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeSamtools test normal samplel gz FINISHED View File O Download File export home app_user framework files WORKSPACE 193 818 1 13346 exomeSamtools_ test normal samplel FINISHED view File O Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeVarAnnota test normal samplel idx FINISHED View File O Download File lexport home app user framework files WORKSP ACE 193 8 18 1 13346 exome Var Annota test normal samplel tsv FINISHED view File O Download File lexport home app user framework files WORKSPACE 193 8181 13346 exomeBaseCover test normal samplel png FINISHED view File O Download File export home app_user framework files WORKSPACE 193 8181 13346 exomeBaseCover test normal samplel tsv FINISHED view File O Download File lexport home app user framework files WORKSP ACE 193 818 1 13346 exomeBaseCover test normal samplel png FINISHED view File O Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeSamtools test normal samplel idx FINISHED View
19. s shown below C Refresh List Target ID Target Level Target Type Target Source ID Target Status Module Name Target Path Actions 87763 sequence file bam 14947 FINISHED Multisample Exome Ver 1 export home app_user framework files WORKSPACE 193 818 1 13346 exomeNovoalign View File O Download File 87762 sequence file html 14947 FINISHED Multisample Exome Ver 1 export home app_user framework files WORKSPACE 193 8 18 1 13346 exomeNovoalign View File 0 Download File 87758 sequence file tsv 14947 FINISHED Multisample Exome Ver 1 export home app_user framework files WORKSPACE 193 818 1 13346 exomeNovoalign View File O Download File 87759 sequence file tsv 14947 FINISHED Multisample Exome Ver 1 export home app_user framework files WORKSPACE 193 8 18 1 13346 exomeNovoalign View File O Download File 87760 sequence file txt 14947 FINISHED Multisample Exome Ver 1 export home app_user framework files WORKSPACE 193 818 1 13346 exomeNovoalign View File O Download File 87761 sequence file tsv 14947 FINISHED Multisample Exome Ver 1 export home app_user framework files WORKSPACE 193 8 18 1 13346 exomeNovoalign View File O Download File 2015 Novocraft Technologies www novocraft com 18 2 You can also view all the files that have been produced by the pipeline by clicking on the View All Output Files button This will open a new tab with the list of all the files not sorted by module a
20. s shown in the following image Target File Target Source Name Target Type Target Status Actions lexport home app user framework files WORKSP ACE 193 8181 13346 exomeNovosort test normal samplel FINISHED view File O Download File lexport homelapp user frameworkifiles WORKSPACE 193 8181 13346 exomeNovoalign gcat set 053 lfastq FINISHED view File O Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeNovoalign gcat set 053 lfastq html FINISHED View File O Download File lexport homelapp user framework files WORKSP ACE 193 8181 13346 exomeNovoalign gcat set 053 lfastq tsv FINISHED view File Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeNovoalign gcat set 053 1lfastq 15 FINISHED View File O Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeNovoalign gcat set 053 lfastq txt FINISHED View File Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeNovoalign gcat_set_053_1 fastq tsv FINISHED View File O Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeBaseCover test normal samplel tsv FINISHED View File Download File export home app_user framework files WORKSPACE 193 818 1 13346 exomeVarAnnota test normal samplel 02 FINISHED view File O Download File lexport home app user framework files WORKSP ACE 193 8181 13346 exomeVa
21. t variants are called and displayed in For more information regarding the VCF format please visit the SAMTOOLS VCF 4 2 specification Chromosome Mame chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chrz Position 43815056 43815080 43815104 115258741 115258765 115258776 115258778 29443719 132181287 132181483 132181519 132181530 209113137 212289016 212530066 212530106 212576894 212578375 212578411 212589860 212589863 212589921 212589825 212652783 212652835 cw Filter QT elele Ia O FA A Reset Length nek Ww rn e GG umm p 4 97023 4 97611 4 97023 4 97023 14 3183 14 3183 Count 3949218063 1042737276 320678088 106924769 32969073 8332279 2817430 1000632 1858888988 3950497693 1043200450 320812085 106892760 32848075 DP 14 SGB 0 378885 EPB DP 14 SGB 0 378885 EPB DP 14 SGB 0 379885 FPB DP 14 SGB 0 379885 RPB DP 8 SGB 0 379885 FPB 1 DP 8 SGB 0 379885 FPB 1 Nat PL PL PL PL PL PL PL PL PL PL PL PL PL PL PL PL PL PL PL 0 1 48 0 140 0 1 48 0 140 0 1 48 0 140 0 1 39 0 214 0 1 39 0 213 0 1 36 0 205 0 1 39 0 218 0 1 39 0 218 0 1 45 0 170 0 1 80 0 185 0 1 39 0 216 0 1 39 0 218 0 1 36 0 222 0 1 51 0 83
22. ysis A Mutisample Exome Ver 1 01 Base Coverage Analysis ai test normal samplel a test normal samplel perBaseCoverageCount taw a test normal samplel bottom30BaseDepthCov png a test normal samplel bedCoverage table taw Ss test normal samplel top30BaseDepthCov png Se Variants E A Mutisample Exome Ver 1 01 Variants Annotation af test normal samplel s test normal samplel ann vcf gz sp test normal samplel snpEffGenes txt sp test normal samplel snpEffsSumrmary html a test normal samplel variantz tegwv E A Muktisample Exome Ver 1 01 Variants Calling Samtools_ a test normal samplel sip normal samplel var vcf gz Log Summary A Mukisample Exome Ver 1 01 ModuleL oc B Summarized Reports Expanding the side bar for each of the project folders reveals the results for each module in the pipeline Clicking the file name will open a new tab in the main panel which will show the files in an easy to understand format The sidebar is repopulated every time a module finishes New outputs will be revealed as the modules are completed 2015 Novocraft Technologies www novocraft com 17 7 0 Using the project job information view C Refresh Job Grid Jab ID Praject ID Jab Start Job Complete Jab Current Status Job End Status Pracess ID 13721 8181 2015 09 09 16 1 2015 09 10 10 3 Alljobs are completed All Jobs Ended 5537 The project information job view shows a more comprehensive list of outputs for each
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