Finding % mapped reads with GraphAligner

[gsc74]

@maickrau As described in Table 1 of GraphAligner, I want to calculate number of correctly aligned reads. In GraphAligner, you have mentioned; "We consider a read correctly mapped if its longest alignment overlaps at least 10% with the genomic position from where it was simulated and evaluate the number of reads correctly aligned", which is similar criteria which minimap2 follows and scripts are provided for evaluation as well.

GAF output of GraphAligner is;

S1_5!chr1!30504300!30508432!+	4142	0	4142	+	>38687>38688>38689>38692	7128	1068	5200	4088	4173	60	NM:i:85	AS:f:3892.1	dv:f:0.020369	id:f:0.979631	cg:Z:22=1I94=1I7=1D15=1D35=1I4=1D74=1I24=1D11=1D57=1I39=1X94=1D24=1X12=1I40=1I40=1D8=1X30=1D126=1D11=1I3=1D132=1I54=1I31=1I117=1I13=1D116=1I84=1I140=1X1=1D120=1I5=1I8=1X87=1I33=1D9=1D65=1I25=1I41=1I26=1I25=1D77=1I70=1D106=1I20=1D28=1D26=1I9=1D27=1D147=1D60=1I52=1D131=1D105=1X8=1I76=1X9=1I37=1I48=1D7=1I62=1D67=1D7=1X36=1I135=1I44=1X5=1I32=1I76=1I24=1D5=1D38=1X1=1X22=1I5=1I216=1I10=1I7=1I11=1I2=1I49=1D111=1X1=1X62=1D34=1D81=

So from GAF ouput, I can get "genomic position from where it was simulated" (S1_5!chr1!30504300!30508432!+) but how do i check alignment overlap?

Could you please provide scripts for evaluation of number of correctly aligned reads?

[BaxW]

you might find this helpful https://github.com/pangenome/rs-peanut