svtyper
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hall-lab
Bayesian genotyper for structural variants
Hi I recently used SVTyper to genotype a big dataset. To do so, I splitted the dataset in several files with 10000 VCF entries each. I did a simple wc...
This is the command I used: svtyper -i sample.vcf -B K1_aln.unique.sorted.bam -l K1.bam.json > K1.gt.vcf And this is the output/error I am getting. Calculating library metrics from K1_aln.unique.sorted.bam... done Writing...
Hi, I've been experiencing a memory error in a couple samples File "/frazer01/software/speedseq-20170419/bin/svtyper", line 1806, in sys.exit(main()) File "/frazer01/software/speedseq-20170419/bin/svtyper", line 1801, in main args.max_reads) File "/frazer01/software/speedseq-20170419/bin/svtyper", line 1527, in sv_genotype...
I noticed that svtyper will force reference evidence, e.g. RP, to 0 if there is no corresponding alternate evidence for that kind _but_ alternate evidence for the other. As an...
We can calculate an estimate for PE/SR ratio based on the read length and insert size. SVs that deviate from this ratio (e.g. few or none of an evidence type)...
Dear svtyper creative team： I have a little trouble using the software and would like to ask for your help. I always encounter the prompt that the RG field is...
Hi， I would like to know which threshold (the sixth colunm "QUAL") is appropriate to use for downstream further filtering of SVs in genotyped svtyper vcf file. 
Hello, author, I used SURVIVOR to merge the results of multiple SV callers, and then used SVTyper to genotype them, but there was always such a warning: "Warning: unsupported SV...
Hello, I've been testing structural variation recently. I called SV with DELLY, Manta and smoove, combined SV results of different callers with SURVIVOR, and finally genotyped with SVTyper. But what...