I am bench-marking the performance of ADAM/Avocado on NGS whole-genome sequencing datasets. I am trying to repeat the tests reported in Frank Nofthat's (author of ADAM and Avocado) thesis, however, I am running into an issue acquiring the dbSNP database to use for Base Quality Score Recalibration.

The Base Quality Score Recalibration command (page 128-129):

adam-submit -- transformAlignments aln.adam bqsr.adam -recalibrate_base_qualities -known_snps dbsnp.adam


requires dbsnp.adam, which is described as "the dnSNP database" (converted to ADAM format) with reference to the NCBI database of genetic variation. This "database" can be found at this FTP site however I do not know which parts of these files to download and convert to ADAM in order to perform this step of the transformation pipeline.

Also, in order to use this genetic variation databaes do I need to make sure that the reference genome of "known variants" is the same genome that the sequencing data was aligned to?

Thank you.

Below I am looking at the .vcf files. I assume this what you want because they can be converted to ADAM format via the adam vcf2adam command.