Over the last year I have been experimenting with using the GATK to analyze the BAM results of FGC11134 men. This has resulted in a very detailed tree for the DF13 subclade. With the experience and newer versions of the software a new workflow has been established to enable hundreds of kits to be efficiently processed and reported.
An important part of the process has always been to maintain a few outgroup samples. These help to draw the line between a variant under FGC11134 and possibly upstream. Using the batch calling functions in GATK allows automated extraction of the ancestral calls, which normally requires a trip to IGV or the like to manually read.
The R-P312 Combo BAM matrix contains a summary of all variants found in the cohort. Each location reports an average confidence for the SNP or INDEL. Then each kit’s read depth are charted for the location. Ancestral calls are marked with a rose colored background and a negative read depth. Derived calls are marked with a green colored background and read depth. When there are alignment issues a heterozygous read is possible. In these cases the depth of both alleles is reported with an amber background.
Any NGS tester under the R haplogroup may submit their BAM for the R-P312 Combo Bam Matrix. Once analysis is complete they will be added to the appropriate haplogroup cluster. Upon inclusion in the workbook they can filter for their truly private high-quality variants, and compare with their near matches.
Individuals wishing to submit their Big Y results should use the “Share BAM” button to create a temporary link, which should then be sent to the email address on the README tab. Full Genomes customers can share their kit with the same address. By doing so you agree to allow analysis and comparison by other researchers interested in the R haplogroup. The file is also available to the individuals responsible for maintaining the ISOGG Y DNA Tree.
Later articles will detail how the R-P312 Combo BAM matrix is generated and some useful examples of how one might look at their results.