Hi

I am trying to compare between my reference fasta file versus some de novo assembly (that includes just a sequences from family of proteins in fasta format after run blast).

I am using the following commands:

minimap2 -cx asm5 --cs /shared2/salmosim/lissa/fasta/TriTrypDB-41_TcruziSylvioX10-1_Genome.fasta CG_1.fasta

when I try to get a stats, I have that results

Number of mapped sequences: 990
Number of primary alignments: 7773
Number of secondary alignments: 7527
Number of primary alignments with >65535 CIGAR operations: 0
Number of bases in mapped sequences: 357654
Number of mapped bases: 489493
Number of insertions in [0,50): 12706
Number of insertions in [50,100): 10
Number of insertions in [100,300): 0
Number of insertions in [300,400): 0
Number of insertions in [400,1000): 0
Number of insertions in [1000,inf): 0
Number of deletions in [0,50): 661
Number of deletions in [50,100): 7
Number of deletions in [100,300): 0
Number of deletions in [300,400): 0
Number of deletions in [400,1000): 0
Number of deletions in [1000,inf): 0

Bur if try to call the SV everyone is 0.

minimap2 -cx asm5 --cs /shared2/salmosim/lissa/fasta/TriTrypDB-41_TcruziSylvioX10-1_Genome.fasta CG_1.fasta CG_1.fasta | sort -k6,6 -k8,8n | paftools.js call -L20000 - > var.txt

I am a beggining in this software, so actually i don't have idea what is happening.

All you help could be a lot of useful to me.

Thank you so much.