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maickrau / GraphAligner

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Finding % mapped reads with GraphAligner #59

Open gsc74 opened 2 years ago

gsc74 commented 2 years ago

@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 commented 2 years ago

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