Big Y BAMs have returned!
FTDNA temporarily suspended issuing BAMs for Big Y in early 2016 to rework their hosting solution. The good news is that the feature was restored in early April 2016. Customers who have been patiently waiting to gain access now have the ability to retrieve the data for third party analysis by companies like YFULL and FGC. The workflow previously shared on this site can also be used to generate a VCF with higher sensitivity settings than those provided by FTDNA.
But something is missing!
As noted in the correction to the previous workflow post, BWA MEM benefits from using paired-end read markers. Enabling this functionality results in better alignment scoring. The new BAMs have the reads named in a way in which BWA is unable to match the pairs. This results in realignment being done as if all reads are single-end sequences. There have also been reports of this causing issues with Ugene, a popular tool for viewing alignments graphically.
BBtools to correct the paired-read names
BBmap contains a large number of utility scripts designed to normalize and fix data issues. One such tool is repair.sh. Designed to repair reads that are disordered or have missing mates, the Java-based shell application includes the functionality needed to rename the reads as expected by BWA MEM. Those using a similar version of the variant discovery workflow can introduce a new step prior to re-alignment quite simply.
bbmap/repair.sh in=interleaved_reads.fq out=fixed.fq outsingle=single.fq
The fixed.fq file contains the Big Y paired-read names needed to allow aligner packages to use the paired-end modes.