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brentp
structural variant calling and genotyping with existing tools, but, smoothly.
hi @brentp, Is there any installation guide where I can implement this on the cluster for parallel processing on centos? Thanks in advance.
@brentp Tried splitting the sample across the nodes using python mpi4py to do the task but on a single node/cross node I do find only one sample is running across...
Hi I installed smoove by conda on linux, but when running it, there are some errors [smoove]: ([E]lumpy-filter) 2021/03/08 15:28:07 /bin/bash: lumpy_filter: command not found Do you know how to...
Hello, everyone! I have some strange error while I run smoove. At begeinning, I run smoove for a sample and it succeeded. But after that, I run smoove for the...
@brentp hi , it report a error when i running smoove. the command is：smoove call -x --name CXL --fasta ../Ref/CXL-1.build.chr.fa --processes 10 --genotype CXL.sort.fixmate.rmdup.bam。 the error is :  Is...
When I try to annotate the results with VEP I get: ``` WARNING: variant 259 on line 280 is too long to annotate: (78162751) WARNING: variant 260 on line 281...
Hello, I met a minor bug: soomve call may translate "+" in into \+, which leads to a panic. It happens in soomve call --outdir , but no problem with...
goroutine 1 [running]: github.com/brentp/smoove/svtyper.check(...) /home/brentp/go/go/src/github.com/brentp/smoove/svtyper/svtyper.go:33 github.com/brentp/smoove/svtyper.Svtyper(0xbd75a0, 0xc00000e110, 0x7ffe7794fd7d, 0x27, 0xc0002895e0, 0x1, 0x1, 0x7ffe7794fd06, 0x22, 0x7ffe7794fd30, ...) /home/brentp/go/go/src/github.com/brentp/smoove/svtyper/svtyper.go:159 +0x1814 github.com/brentp/smoove/lumpy.Main() /home/brentp/go/go/src/github.com/brentp/smoove/lumpy/lumpy.go:347 +0x44f main.main() /home/brentp/go/go/src/github.com/brentp/smoove/cmd/smoove/smoove.go:124 +0x1ce
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...
Brent, do you have any suggestions for filtering a multisample smoove VCF for duphold? Just filtering the first sample will extraneously exclude some samples, and including any sites (FMT/DHFFC[*], e.g.)...
