First genomic coordinate that Nanopore read aligns to

Question

[K2020]

I aligned Nanopore reads to a genome of interest and outputted a sorted BAM file. I want to determine the genomic coordinate that corresponds to the first base of each aligned read aka where in the genome the start of each read aligns. Any suggestions?

Answer 1

[Dave Carlson]

From the SAM file specification (section 1.4):

1. POS: 1-based leftmost mapping POSition of the first CIGAR operation that “consumes” a reference base (see table below). The first base in a reference sequence has coordinate 1. POS is set as 0 for an unmapped read without coordinate. If POS is 0, no assumptions can be made about RNAME and CIGAR.

In other words, the first position of the alignment should be the fourth field in the SAM/BAM file.