svtyper
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hall-lab
Bayesian genotyper for structural variants
I have about 100 samples, and i I runned Lumpyexpress with -p and got the sample1.vcf, sample2.vcf, sample3.vcf, et al. lumpyexpress -B sample1.bam -S sample1.splitters.bam -D sample1.discordants.bam -P -o sample1.vcf...
Hi I'm trying to run SVTyper on the vcf file I got after running Lumpyexpress. Here is the code that I am using: svtyper \ -i sv.vcf \ -B sample.bam...
Hi, After running Svtyper,We can get DP and other information about a variant. I want to know how to get the DP by Svtyper?
Hi Colby, We are using Speedseq 0.1.2 to process the whole genome For ex: NA12877. We are getting many calls with QUAL = 0. Can we just filter them from...
svtyper uses AO and RO, but the spec has now settled on AD for ref, alt depths. this would simplify getting alt depths from a VCF without caring if it's...
We port svtyper to python3. We add svtyper-pms script which will parallelize by individuals (instead of parallelize by batch for an unique individual, like svtyper-sso). This script will launch in...
Hi, I'm running svtyper on the output of Delly2. Then I got these error messages: ``` Traceback (most recent call last): File "/home/work01/tools/SVTyper/svtyper/svtyper", line 1808, in sys.exit(main()) File "/home/work01/tools/SVTyper/svtyper/svtyper", line...
Hello, I am using svtyper on the results of a lumpy somatic vcf and am therefore running it with 2 bwa-mem bams and 2 split reads bam files. I find...
Hi, I wonder if qual column represents Phred-scaled probabilities? If so, Is it logical to filter out any quality score smaller than 10 to get at least 90% accuracy? Best,...
I'm seeing samples genotyped as follows: `GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:1:4.77:0,0,0:0:0:0:0:0:0:0:0:0:0:.` It seems like this should be reported as a null genotype instead...
