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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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targeted sequencing call SV #131

Open tyyiyi opened 4 years ago

tyyiyi commented 4 years ago

Hi, I am using smoove to call SVs. I have about 50 samples, which are tumor-normal pairs of human. Their sequencing depth is about 1000X, which is targeted sequencing. I want to know if I can use smoove to call SVs on my data, should I construct an exclude file based on my own targeted sequencing bed file? smoove call --outdir $output --name $fname --exclude $offtarget_region --fasta $ref -p 1 --genotype $tumor.MarkDuplicates.bam $normal.MarkDuplicates.bam

brentp commented 4 years ago

that should work, though I'd use the exclude files recommended or make sure that your off-target does not contain bases just proximal to your capture regions.

tyyiyi commented 4 years ago

So how many bases do you think are the adjacent bases of the target region? 500bp? 

---Original--- From: "Brent Pedersen"<notifications@github.com> Date: Wed, Sep 23, 2020 22:44 PM To: "brentp/smoove"<smoove@noreply.github.com>; Cc: "Author"<author@noreply.github.com>;"tyyiyi"<863099940@qq.com>; Subject: Re: [brentp/smoove] targeted sequencing call SV (#131)

that should work, though I'd use the exclude files recommended or make sure that your off-target does not contain bases just proximal to your capture regions.

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brentp commented 4 years ago

yes, or 1000 even.