svtyper

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The error log shows that it can not open the alignment file if I put the bam file name together with comma separated. SVtyper works well with it.

verne91

I'm benchmarking SVTyper and making PR curves. I have two questions to make sure I'm comparing SVTyper as I should. I'm using the QUAL field to make the curve. I...

jmonlong

Hi Dave, I read you script, and noticed that RO is calculated by ref_seq+ref_span. and ```ref_seq``` is calculated by the following code. ```python # svtyper/svtyper/singlesample.py line 255 to 259 is_ref_seq_A...

xyw1

I've been spending the last few days becoming familiar with Lumpy + SVtyper, and starting to get the hang of them. I've run into an issue that I haven't been...

calhoujd

Hi, I noticed that the default is unlimited for 'max_reads' in classic svtyper. But why are there still some ungenotyped SVs in the output ? How should I deal with...

lss1227

Best FORMAT field for filtering SVTyper Output

2

Hi Dave, I'm running SVTyper on output from Lumpy for hg38 whole genome samples with 50x depth, interested in finding Deletions and other SVs with a low false-positive rate. The...

andrewSharo

Using svtyper for other sv callers

2

Hi, I wonder if anyone used svtyper to genotype pindel and delly outputs? Do I need to modify their outputs to make svtyper work or should I give their outputs...

MehmetGoktay

This script is an answer to the lack of multi threading capacity in svtyper, issued here: #92. It is only in part an answer to #91 as this script only...

dvanderleest

Question

2

I as wondering if svtyper does "joint genotyping" of multiple samples, analogous to what GATK does for SNPs? Does svtyper do break-point resolution? For example, if I have a population...

ldorozco

Lack of support for (b)gzipped vcf files and analysing only part(s) of the files (region support)

4

svtyper currently doesn't support the (b)gzipped file format. This leads to the following type of error. Command: `svtyper -B $(ls analysis/temp/*/*piped.bam | paste -sd",") -i vcf/StructuralVariants.raw.lumpy.sorted.vcf.gz -l my.bams.json > vcf/StructuralVariants.gt.vcf`...

dvanderleest