ADAM: Fast, Scalable Genome Analysis
A talk I gave at the 1st plenary of the Global Alliance for Genomics and Health
I gave a talk about ADAM at the Global Alliance for Genomics and Health first plenary meeting at the Wellcome Trust Sanger Institute.
Introduction to Base Quality Score Recalibration (BQSR)
Playing with matches and CIGARs
Aligned reads in a SAM or BAM file typically have a Compact Idiosyncratic Gapped Alignment Report (CIGAR) string that expresses how the read is mapped to the reference genome.
When I first read the CIGAR operator table (above), I was confused by two things:
- the match,
M, operator description, “alignment match (can be a sequence match or mismatch)“, struck me as odd.
- the relationship between the
Xoperators isn’t explained in the spec.
I hope this blog post helps others with the same questions.[Read More]