Big-Y BAM Analysis Tool

[felix]

After receiving the BigY .BAM file, if anyone wishes to extract all information from it, i.e., autosomal, x-dna, mtdna and additional y-snps, they can use this tool which is able to run on a normal windows system just using a simple command.

Download: Big-Y BAM Analysis Tool (~ 3.1 GB)

Usage:

• Extract the compressed download file Big-Y BAM Analysis.zip.
• Extract the BAM zip download and copy your .bam file into the extracted folder.
• Open command-prompt, change directory to the extracted folder and execute the below command

bigybam <BigY BAM file>.bam

After around 4-8 hours (depending on your computer speed), the output will be available inside a sub-folder called 'out'. Also ignore any error with file-not-found, esp. on the last completion screen.

Output:

• complete_bigy_autosomal.csv - contains all identified SNPs in BigY BAM file.
• complete_bigy_mtdna.fasta - mtDNA found in BigY in FASTA format.
• complete_bigy_x.csv - contains all identified X-DNA SNPs in BigY BAM file.
• complete_bigy_y.csv - contains all identified SNPs in 23andMe format with RSIDs.
• ftdna_bigy_autosomal.csv - contains only SNPs tested by FTDNA that are found in BigY BAM file.
• ftdna_bigy_mtdna.fasta - mtDNA found in BigY in FASTA format (duplicate output - same as complete_bigy_mtdna.fasta).
• ftdna_bigy_x.csv - contains only X-DNA SNPs tested by FTDNA that are found in BigY BAM file.
• ftdna_bigy_y.csv - contains all identified Y-SNPs in FTDNA table format.
• ftdna_bigy_ysnps.txt - contains all identified Y-SNPs separated by comma.

Link: http://www.y-str.org/2014/04/big-y-b...ysis-tool.html

[Varego]

Wow. Just...wow.

Thank you!

[JohnG]

Felix,

You are amazing!

[felix]

Just optimized the download with a User Interface (instead of a command-line), reduced the size and made it clear on the download that it works only in 64 bit windows systems.

Download: Big-Y BAM Analysis (64 bit).zip (1.47 GB)

[MitchellSince1893]

Error Message

I downloaded link you provided and I have 64 bit machine but I get this error message when I click BigY BAM Analysis.

Microsoft.NET Framework
Unhandled exception has occurred in your application. If you Click Continue, the application will ignore this error and attempt to continue. If you click Quit, the application will close immediately.
Cannot load Counter Name data because an invalid index.


I clicked continue but the buttons are grayed out and I can't select my BAM file.

[felix]

I downloaded link you provided and I have 64 bit machine but I get this error message when I click BigY BAM Analysis.

Microsoft.NET Framework
Unhandled exception has occurred in your application. If you Click Continue, the application will ignore this error and attempt to continue. If you click Quit, the application will close immediately.

I clicked continue but the buttons are grayed out and I can't select my BAM file.

There is one other requirement is that you should have .Net 4.0 for the Windows version to work.

You can get it from here: http://www.microsoft.com/en-au/downl....aspx?id=17718

Just let me know how it goes. It would be great to hear if it works as expected.

[MitchellSince1893]

I already have Net 4.0 for Windows installed but still not working.

I uninstalled and reinstall this program but it didn't fix the problem.

[wkauffman]

JRE not executing

On 8.1 with 8gb of RAM the original download fail so kick off the JRE

Creating Sequence Dictionary for Human Reference Genome ...
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

[felix]

On 8.1 with 8gb of RAM the original download fail so kick off the JRE

Creating Sequence Dictionary for Human Reference Genome ...
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

The original download mixes 32 bit and 64 bit executables and works only on 64 bit - which I modified in the new download making everything as 64 bit. Also, 32 bit JRE cannot have more than 1536 MB of RAM.

On the original download, you can try reducing the heap size. There will be a batch file bigybam.bat. You can edit it in notepad or any text editor to change the value from 1536 to something lower 1024. Just find and replace 1536 to 1024 and execute the command again.

[felix]

I already have Net 4.0 for Windows installed but still not working.

I uninstalled and reinstall this program but it didn't fix the problem.

The Windows GUI is not really required for the working of this application. It simply constructs the batch file required to execute. You can still use the old fashioned way using the command-prompt (attached).

extract and copy the bigybam.bat into the folder. using command prompt change directory to that folder and execute

bigybam <bigy-bam-file>.bam

Meanwhile, I will investigate why it is failing.

[felix]

I already have Net 4.0 for Windows installed but still not working.

I uninstalled and reinstall this program but it didn't fix the problem.

I handled the error and updated the windows user interface.

Copy this into the folder and it should work.
Let me know how it goes.

[wkauffman]

The original download mixes 32 bit and 64 bit executables and works only on 64 bit - which I modified in the new download making everything as 64 bit. Also, 32 bit JRE cannot have more than 1536 MB of RAM.

On the original download, you can try reducing the heap size. There will be a batch file bigybam.bat. You can edit it in notepad or any text editor to change the value from 1536 to something lower 1024. Just find and replace 1536 to 1024 and execute the command again.

The clean 64-bit version is cranking away on the SSD drive. I probably should have rebooted and turned on the overclocking to cut the time by 10%.

[MitchellSince1893]

I handled the error and updated the windows user interface.

Copy this into the folder and it should work.
Let me know how it goes.

It's doing something now...screen says

"Initial Cleanup..."
Sorting "C:\..."

Indexing the Sorting BAM file ...

Indexing the Human Reference Genome ...

Creating Sequence Dictionary for Human Reference Genome...

Thanks for your assistance!

I'll let you know how it turns out.

[felix]

The latest download with the updated UI (as in post #11), a fail-back console batch file.

Download: Big-Y BAM Analysis (64 bit).zip

[Հայկո]

Thank you Felix! I was able to extract all the information from my Big Y BAM file with no error messages or problem. I have a 3 year old HP 64bit PC. I ran the exe file at 8:30pm last night, the "out" file was ready 6:00am this morning.