svtools
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hall-lab
Tools for processing and analyzing structural variants.
I ran the following command: svtools lsort P001_WD11-smoove.genotyped.vcf.gz P001_WD12-smoove.genotyped.vcf.gz P001_WE11-smoove.genotyped.vcf.gz | bgzip -c > sorted.vcf.gz And I get this error: Traceback (most recent call last): File "/home/ubuntu/progs/miniconda3/envs/smoove/bin/lsort", line 70, in...
I'm trying the dockerhub image with svtools and running as follows: ``` singularity exec -e --no-home docker://halllab/svtools:v0.5.1 svtools vcftobedpe -i $inputvcf -o vcftobedpe.bedpe -t tmp singularity exec -e --no-home docker://halllab/svtools:v0.5.1...
Hello, I installed svtools, cnvnator, root, lumpy-sv by using "mamba install -c conda-forge -c bioconda root cnvnator lumpy-sv svtools", the installation is smoothly. When I run "svtools copynumber --cnvnator cnvnator...
Hi! I am trying to convert a Manta-called VCF structural variants file to bedpe format. here the code I use `svtools vcftobedpe -i somaticSV.vcf -o myFile.bedpe` and there the error...
Hi, I was trying to modify [sv-pipeline](https://github.com/hall-lab/sv-pipeline/blob/master/scripts/Post_Merge_SV.wdl) to be able to classify variant calls of a smaller cohort. calc_params would fail if deletions are not present in the naive Bayes...
`setup.py` was using the latest stable release for dependencies without a version specified; this resulted in incompatible dependency versions. This commit changes some versions and ensures all dependencies have a...
i have the following vcf record that i believe is not correctly represented in the result when using vcftobedpe: ``` 6 57184412 Pipeline_TRA_6_57184412 N N]8:36752983] . PASS END=36752983;Callers=manta,delly;NumCallers=2;CHR2=8;SVTYPE=TRA;STRANDS=++;delly_CIEND=-2,2;delly_CIPOS=-2,2;delly_PE=3;delly_MAPQ=60;delly_SRMAPQ=60;delly_SR=12;delly_SRQ=0.985981;delly_CE=1.93075;delly_CT=3to3;delly_PRECISE;delly_SVMETHOD=EMBL.DELLYv0.8.2;delly_INSLEN=0;delly_HOMLEN=2;delly_RDRATIO=1.17045;delly_SOMATIC;manta_CIPOS=0,1;manta_MATEID=MantaBND:136490:1:6:0:0:0:1;manta_HOMLEN=1;manta_HOMSEQ=A;manta_BND_DEPTH=70;manta_MATE_BND_DEPTH=96;manta_SOMATIC;manta_SOMATICSCORE=90;NumCallersPass=2 delly_GQ:delly_FT:delly_RC:delly_RCL:delly_RCR:delly_CN:delly_DR:delly_DV:delly_RR:delly_RV:manta_PR:manta_SR 10000:PASS:117:50:63:2:36:3:28:16:44,3:55,16...
While we merged VCF files, the subcommand lmerge in svtools is the same as l_merge.py scripts included in LUMPY? Are the result of merged VCF files same？
Just wanted to bring up that running lsort/lmerge/prune pipeline seems to still result in a number of overlapping calls (>50% Reciprocal overlap for about 1000 variant pairs in my filtered...
Hi, I tried to merge files from 206 samples, and encountered this error. Do you have any idea where should I look at? The merging job ends prematurely, and left...
