No Duplications output

[hhuili]

Hi,

I have recently used svim-asm to identify SVs on hundreds of virus genome assemblies.

Here is my code:

minimap2 -a -x asm5 --cs -r2k -t $threads $reference $genome_dir/${assembly}.tidy.fa > alignments.sam
samtools sort -m4G -@4 -o alignments.sorted.bam alignments.sam
samtools index alignments.sorted.bam
svim-asm haploid --query_names ./ alignments.sorted.bam $reference

I merged the outputs and found that there are only INS and DEL two types. I'm wondering if svim-asm identified Duplication and Contraction as INS and DEL, respectively? It is similar to this issue #6 .

Furthermore, same as the #14 , svim-asm doesn’t give the coordinates of query genome in the output vcf file. It would be very informative if it gives query coordinates as well.

Thanks in advance!

Best,
Huihui Li