
• 0 views
•
link
In the gam file format specification, it says it has 12 mandatory fields. But in the example it has more columns with some cigar strings. What does they stand for? (cg:Z:6M and cg:Z:7M in the example file) Example file in the link is the following
read1 6 0 6 + >s2>s3>s4 12 2 8 6 6 60 cg:Z:6M
read2 7 0 7 + >s2>s5>s6 11 1 8 7 7 60 cg:Z:7M

https://github.com/lh3/gfatools/blob/master/doc/rGFA.md#the-graph-alignment-format-gaf
GAF is a TAB delimited format for sequence-to-graph alignments. It is a strict superset of the PAF format.
PAF : https://github.com/lh3/miniasm/blob/master/PAF.md
A PAF file may optionally contain SAM-like typed key-value pairs at the end of each line.
Log in to answer this question.