svtyper

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Dear @brentp When calling population CNVs, I would use different tools (e.g., Lumpy. Delly, and Manta) to call SVs for each sample, and thus I will get three VCF files...

biozzq

Trying to run svtyper on a vcf produced by lumpy, using the docker container found via: docker pull halllab/svtyper:v0.7.1-3c5218a ``` $ docker run -v "/blue/project/trios/data:/blue/project/trios/data" halllab/svtyper:v0.7.1-3c5218a svtyper -B /blue/project/trios/data/trio3F15.sorted.bam -l...

tirohia

SVtyper with long reads

7

So - I'm trying to generate SV frequencies from long read data (ONT) aligned with a split-read aligner (BWA MEM) using SVtyper, but I keep getting an error: Error: Traceback...

timp0

I was trying to use [`samplot`](https://github.com/ryanlayer/samplot/issues/101) on my various call sets; however, for Pindel, all of the variants are homref so I and was directed here. A couple of my...

moldach

annotate translocations with svtyper

2

Hello, I was wondering wether it is possible to annotate translocations with svtyper. In the header of the svtyper vcf output I see these types of SVs ##ALT= ##ALT= ##ALT=...

jazberna1

brentp

Hello, I tried to install the tool using pip install git+https://github.com/hall-lab/svtyper.git and it seems to error out because of the numpy version is not compatible with the python version required...

kgaonkar6

    I'm curious about the output from merge multiple samples using svtyper and lmerge. It seems like different from SNP vcf from GATK. How can I understand the REF...

xujinshengjsxu

wentgithub

header parsing can't handle ">" in description

3

e.g. this header from the genome in a bottle truth set fails: ``` ##INFO= ```

brentp