The BIG Y test from FTDNA

[Dorianfinder]

The BIG Y technical details have been posted as follows:

• Targeted Non-recombining Y-DNA sequencing
• Illumina HiSeq 2000
• 55X to 80X average coverage
• Around 11.5 to 12.5 million base-pairs of reliably mapped positions of non-recombining Y-Chromosome
• Analyzed using Arpeggi genome analysis technology for improved variant calls
• The VCF files will be available for download on your results page. Raw results will be formatted in .BAM format. The standard FASTQ file from the Illumina test itself may also be requested by advanced users by contacting FTDNA.

[h=5]Y-STR results from BIG Y testing? You can request the .BAM file of your results and use 3rd party tools to get Y-STR results.[/h]1. Dr Mittelman stated that "thousands" of BIG Y orders were purchased during the initial sale and added "FTDNA have more Y than anyone else"

2. Dr Mittelman advised that the BIG Y test sequences around 13.5 million bases on the Y-chromosome and provides results for between 11.5 and 12.5 million positions. It is not possible to give a precise figure because NGS results vary from person to person. This is an improvement on the spec that was advertised when the pre-sale was announced in November when a figure of 10 million bases was quoted.

3. When the BIG Y pre-sale was announced the coverage was advertised as 60x (the number refers to the number of times the Illumina machines read the sequence the more reads the better). The information on the BIG Y FAQ page has since been updated and the coverage is now being advertised as “55x to 80x average coverage”.

4. BIG Y coverage varies from person to person but it is expected that results will be provided for between 25,000 to 35,000 known SNPs per person.

5. A separate list of novel variants (newly found SNPs), defined as variants which differ from the reference sequence and which are not seen in the FTDNA SNP database, will be provided with each BIG Y result. The genome reference co-ordinates will be provided which will allow comparisons with SNPs identified in tests from the only other company that provides NGS (next generation sequencing), Full Genomes Corporation. Dr Mittelman does not yet know how many novel SNPs to expect per person. There is currently no function to compare novel variants in the database, but the test is very much a work in progress and he is open to suggestions for new ideas.

White paper
Dr Mittelman advised that once all the data has been through quality control FTDNA will then produce a white paper which will provide information on some of the technical details of the test. The paper will cover performance metrics, value proposition, etc, and they also hope to look at mutation rates, something which is of great interest to the genetic genealogy community and a subject of considerable debate and disagreement! The paper should be out in the next four to six weeks or so.

The new Y-tree
BIG Y data is currently being released using the now very out-of-date and somewhat irrelevant 2010 Y-tree. Bennett Greenspan, the Chief Executive Officer of Family Tree DNA, advised in the webinar that they have had teams of people working on the new tree in collaboration with the Genographic Project. The new tree will be fully integrated with Geno 2.0. The tree needs to be ready from both the technical point of view and the graphical interface, and it seems that it is the latter which is proving more problematic. The tree is not dependent on the release of a scientific paper. Bennett advised that it might be ready in the “next several weeks”. When the new tree is finally launched, SNPs from the BIG Y will be automatically mapped on the new tree.

Comparison with Full Genomes?
When the BIG Y raw data files become available it will be possible to do a comparison of the two tests. For comparisons of the available SNP tests, including the Geno 2.0 and Chromo 2 chip tests, see the SNP testing comparison chart in the ISOGG Wiki.

source: http://cruwys.blogspot.co.uk/2014/03/the-big-y-roll-out-snp-tsunami-is-on.html

 

[Sile]

Is this Big Y test just jumping on the findings of the extra SNP's that the volunteers of ISOGG found over time? or have they more

 

[Dorianfinder]

Big Y AddOn for Google Chrome

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Big Y AddOn is a chrome browser extension that adds additional functionality to Family Tree DNA's Big Y results and plots the results on up-to-date Y-DNA Trees.

The extension adds a number of features to BigY Results

• Download results as Y-DNA markers
• Download the Table as CSV - (Comma Separated File which can be opened in Excel)
• Auto-Populates SNPs into MorleyDNA Y-Tree for easy analysis.
• Highlights Positive and Negative SNPs in ISOGG Y-Tree.

Extension Page: https://chrome.google.com/webstore/d...doediffhcdfdmj
Source code and project page: http://www.y-str.org/tools/big-y-addon/

Comments and suggestions welcome.

Work in progress

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The ability to see your results on ISOGG, Morley's experimental tree & FTDNA is a great tool. However, there still appears to be much more work to be done to refine the haplogroup predictions. For now, folks should still rely on the haplogroup projects as most of them have the expertise to tease out the proper placement for folks.


link http://forums.familytreedna.com/showthread.php?t=34530

 

[Dorianfinder]

Big Y - YFull - Y-Chr Sequence Interpretation Service

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Here is an example of results from YFull after a Big Y (FTDNA) customer sent his .BAM results to them.
Big Y - YFull - Y-Chr Sequence Interpretation Service

Just to clarify:

1) YFull does not currently charge for its service to "researchers" (i.e., to anyone who is willing to let their results become anonymously public).

2) YFull is not a competitor of FTDNA but rather more like an academic partner: Its work helps FTDNA construct a new, more elaborate haplotree from Big Y results.

 

[Dorianfinder]

Felix Chandrakumar mentions on his blog that the Big Y test results includes most of mtDNA, 400+ Y-STR and 50 000 Y-SNPs. The initial sale price of the Big Y test was US$495.

 

[Dorianfinder]

Big-Y BAM Analysis Tool

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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

Code: 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

The latest download with the updated UI, a fail-back console batch file. Download: Big-Y BAM Analysis (64 bit).zip

 

[Dorianfinder]

Big-Y BAM Analysis Tool

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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

Code: 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

The latest download with the updated UI, a fail-back console batch file. Download: Big-Y BAM Analysis (64 bit).zip

After having done the analysis the FTDNA identified SNPs should go from 36 500 SNPs to around 43 000 SNPs
and your FTDNA named SNPs should increase from 590 SNPs to around 1 200 SNPs.

This analysis tool by Felix is free!