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davidebolo1993 / VISOR

VarIant SimulatOR for short, long and linked reads
GNU Lesser General Public License v3.0
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VISOR SHORtS for simulating pair-end data #28

Closed lx-1011 closed 1 year ago

lx-1011 commented 1 year ago

Dear @davidebolo1993 , Thanks your for this useful tool. I have a question about simulating illumina sequencing data using VISOR SHORtS. Firt, using the same insertion bed file for simulating long-read and short-read sequencing data, i found that most of insertion could not be simulated in short-read data, like that image image image

VISOR HACk -g ref.fa -b ins.bed -o ./ins.hack.out

VISOR SHORtS -s ins.hack.out/ -b shorts.laser.simple.chr1.bed -g ref.fa -o ./SR.ins.laser.out --threads 10 --coverage 50

Do you have any suggestions on that? Thank you so much Lixin

davidebolo1993 commented 1 year ago

Hey @lx-1011,

I would say that this is expected since short reads have limitations with large SVs and are splitted at breakpoints. Highlighting soft-clipped bases should help.

Let me know if you need help,

Davide