Frequently Asked Questions

1. How do I remove my account?

   Account removal is currently a back-end process. Use Contact Us to request the User associated with your email to be removed by the site's administrator. To speed the process make sure that you remove any samples from your My Samples home page. The "Remove" process ensures that all raw data files are also purged from the object repository as well as the reporting data. Once all Samples have been removed, your User account can be safely removed.

2. Why am I assigned to Haplogroup X? On another site I am Haplogroup Z.

   The primary cause of this issue comes down to the differences in Y DNA trees. The Shared SNPs report tab will detail the calls that led to your sample being assigned to the position in our tree. As long as there are not two branch levels where most of the markers are coded as negative calls, the sample is correctly positioned. If you see many levels where no calls are reported, it may be a recurrent marker in the Sample's signature causing interference with the machine learning routines. The best course of action for these is to add the BAM file for a high-coverage discovery test like Big Y or WGS.

   Occasionally, it is because the wrong set of raw data files were submitted for the subject. The best course of action here is to delete the files already submitted and upload them again. The system will import the files again and recalculate the haplogroup when finished.

3. Do I need to submit my BAM?

   This is a nuanced question. While technically not required, submitting your raw BAM file (containing the sequencing reads) offers several significant advantages for our analysis.

   • Enhanced Analysis:
     • Realignment: Our analysts can realign your data to the latest Y chromosome sequences from the Human Pangenome Project, ensuring the most up-to-date and accurate results.
     • Improved Variant Calling: Using your raw data allows us to perform joint calling with other related individuals, potentially identifying variants missed in individual analyses.
     • Data Preservation: Having a backup of your raw data in our systems provides an extra layer of protection against data loss.
   • Third-Party Analysis: If you plan to explore your results with other researchers or services, your BAM file provides them with the most complete and flexible dataset for their own analyses.
   • Important Notes:
     • Data Format:
       • WGS: If your data is from Whole Genome Sequencing (WGS), we recommend using the hs1/chm13v2.0 reference genome. This minimizes unmapped reads on the Y chromosome in GRCh37 and GRCh38.
       • Targeted Sequencing: For targeted sequencing like FTDNA's Big Y, which focuses on specific regions of the Y chromosome, realignment is not necessary. All reads are within CM000686.2 on GRCh38.
     • Data Preparation:
       • Filtering: Before submission, please filter your BAM file to include only reads from the Y chromosome (chrY) and optionally the mitochondrial DNA (chrM).
       • Tools: You can use tools like samtools or sambamba for this:
       Bash Command - samtools
       samtools view -o chrYM.bam original.bam chrY chrM [optionally for GRCh 38: chrY_KI270740v1_random]
       Bash Command - sambamba (preserves read mates)
       sambamba view -F "ref_name == 'chrY' or mate_ref_name =='chrY' or ref_name == 'chrM' or mate_ref_name =='chrM'" -f bam -o chrYM.bam original.bam
     • Data Submission:
       • Cloud Storage: We recommend uploading your BAM file to a cloud storage service like Dropbox and sharing the link via our submission form. This ensures secure and efficient data transfer compared to direct uploads.

   Disclaimer: While we value the submission of raw data, we understand that some users may prefer not to share their BAM files. Our analysis can still be performed effectively using Variant Call Files (VCFs), although with some limitations in terms of flexibility and the potential for enhanced analysis.