svtools
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hall-lab
Tools for processing and analyzing structural variants.
Hi, I have run `svtype`, `svtyper-sso` and `svtools genotype` on the same dataset. I found the variants with GT of ./. had discrepant values in other genotype fields. > svtools...
Hi, I'm trying to use svtools classify as suggested in Classifier.md After following all the steps in your tutorial I've successfully generated a VCF with SV calls for ~85 samples....
Hello, we are using svtools to creating bedpe files that originate both from MANTA and Delly. In some cases, MANTA generates a structural variant call that looks like this: `chrX...
Hello, I wanted to get some clarifications about these two steps in the [Tutorial ](https://github.com/hall-lab/svtools/blob/master/Tutorial.md) that seem to be doing similar things. I notice that issue #12 points out that...
After running lmerge on a large number of samples, I see that about 25% of variants have used ALG=SUM. Perhaps [this](https://github.com/hall-lab/svtools/blob/master/svtools/lmerge.py#L273) (`if miss == 0`), could be instead something like:...
Hi, I'm using svtools-0.4.0 published on bioconda, and I found that breakpoint positions in BEDPE file converted from lumpy vcf output using `vcftobedpe` seem to be 1-based. For example, the...
Dear, I'm confused in order to use the parameters of svtools... in lmerge.... After use lsort, I want to merge al my samples wit lmerge. But I dont know how...
Dear all, I run all my samples with lumpy, the lumpy developers recommended me use the -P option in order to run svtools lsort. All my 808 samples are ran...
I have been using the svtools pipeline on my datatset where `lsort` `lmerge` and `genotype` have been implemented successfully. The coordinates file has been generated from the `lmerge` vcf file....
