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asylvz / SVarp

Phased structural variant discovery in pangenomes
MIT License
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Any alignment tools recommended? #1

Closed Zoeyoungxy closed 7 months ago

Zoeyoungxy commented 8 months ago

Hi, So excited to see this pangenome-based SV caller! Would you please give me some detailed information to use svarp?

  1. An alignment file in .gaf format is needed, I wonder which aligner is suitable for svarp, GraphAligner or minigraph? Is there any tools and parameters recommended to align the sequence to a GFA graph ?
  2. Does the input parameter --fasta (-f) mean the query sequence? The .gaf file is already provided, why do we need the fasta file as well? Is it to provide insertion sequence information?

Thanks

-Zoey

asylvz commented 8 months ago

Hi Zoey,

  1. You can use both but we mostly tested with minigraph due to runtime related reasons. This is a sample command for alignment: "minigraph -cx lr XXX.gfa XXX.fasta.gz --vc -t 32 > OUT.gaf"
  2. Fasta is needed for the local assembly that we use

Best, Arda

Zoeyoungxy commented 7 months ago

Hi Zoey,

  1. You can use both but we mostly tested with minigraph due to runtime related reasons. This is a sample command for alignment: "minigraph -cx lr XXX.gfa XXX.fasta.gz --vc -t 32 > OUT.gaf"
  2. Fasta is needed for the local assembly that we use

Best, Arda

This is very helpful! Thank you