svtyper
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hall-lab
Bayesian genotyper for structural variants
Hi, I'm hoping to be able to run SVTyper in a generic mode on any SV tool. I have tried running SVTyper on Manta and SvAbA vcfs, and am running...
- This pull requests fixes issue #103 where svtyper fails with a KeyError due to the input VCF missing "CIPOS" information. - Fix consists of adding a try block around...
Hi, I'm trying to use svtyper on my mac and after installation when I try to run the executable I get this error: % svtyper Traceback (most recent call last):...
Dear, thanks a lot for developing this tool. I already found between the issues that sometimes svtyper reports REF calls without support (`10/0:0:4.77:0,0,0:0:0:0:0:0:0:0:0:0:0:.`) when there are no reads aligning in...
Hello, I run the svtyper by using lumpy SV vcf file as a input. When I saw the genotyped sv file, it contained "./.", "0/0 genotype information.  1. In...
```[ 2019-04-29 10:13:21 ] Collecting breakpoints Traceback (most recent call last): File "/home/cnsun/.local/bin/svtyper-sso", line 11, in load_entry_point('svtyper==0.7.0', 'console_scripts', 'svtyper-sso')() File "/home/cnsun/.local/lib/python2.7/site-packages/svtyper/singlesample.py", line 848, in cli sys.exit(main()) File "/home/cnsun/.local/lib/python2.7/site-packages/svtyper/singlesample.py", line 841,...
Dear svtyper team, Do you intend to provide a python3 version of svtyper. I am using svtyper within a pipeline written in python3 and incorporating a python3 version would greatly...
Hi, The old link doesn't work anymore. Here is the new link: https://www.nature.com/articles/nmeth.3505
Hello, While trying to cal SVs from a Lumpy output, I receive this error: Error: invalid FORMAT field, "+" Here is my code: /Library/Python/2.7/bin/svtyper -B LA1303_int2sort.bam -i LA1303_lumpy.vcf > LA1303_svtyper.gt.vcf...
Hello, I am using smoove to call SV. Some of the information in the output file it produces makes me confused. I asked brentp and he told me that the...
