smoove
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brentp
structural variant calling and genotyping with existing tools, but, smoothly.
I just got smoove installed today and tried running it for the first time. I downloaded some bam files and a reference from a galaxy history where I'd already analyzed...
Hi, I am using smoove to call SVs in ~170 samples. I ran through the whole pipeline and the final "square" file only contains variants up to chr 2. I...
Hello, I have several BAMs from the same capture and pre-processing was the same for all of them. For some of the BAMs, they are fine with smoove but for...
currently the VCF still has AO, RO from svtyper. The spec now has AD as the field to store the ref and alt alleles.
this can take CI into account and allow the user to know the population frequency of a given SV.
Hi @brentp, I ran smoove v0.2.2 using singularity and I run it as part of a nextflow process. When I execute with small sample size (i.e. 30, 100, and 300),...
this is difficult for cloud as it requires accessing the BAM/CRAM files directly.
Hello, I notice that there appears to be some cnvnator scripts in smoove, including a 'smoove cnvnator' command. How do I got about running these and incorporating them into a...
Hello there, I just incorporated your tools into my SV calling pipeline and it is working great. I did run into a panic error that was a bit confusing, but...
lumpy gives ths SU of 5. svtyper gives it only 3 so it should be removed. This is the case for a lot of false positives. ``` 1 865249 1...