metasv
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bioinform
MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
ERROR 2022-11-16 09:35:06,865 run_spades_single- Caught exception in worker thread Traceback (most recent call last): File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/site-packages/metasv/run_spades.py", line 75, in run_spades_single retcode = cmd.run(cmd_log_fd_out=spades_log_fd, timeout=timeout) File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/site-packages/metasv/external_cmd.py", line 20, in run...
Hi and thanks in advance for your help! While running MetaSV, it got stuck while running spades. There are a few 'OSError: [Errno 13] Permission denied' errors during the run_spades_single...
Hi, I am trying a complete run of MetaSV 0.5.4 (installed from bioconda) using all 2 SV detectors (pindel and breakdancer), soft-clips based analysis, and local assembly. And got this...
Error after running Metasv；can you give me some suggestion? $METASV --pindel_native /bak01/yangqj/pindel/20220116/vcf_format/ps0001/ps0001_* --cnvnator_native /bak01/yangqj/cnvnator/ps0001.call --reference /bak01/yangqj/Metasv/hg19.fa --outdir out --sample ps0001 --filter_gaps --minsvlen 500 --maxsvlen 500000 --disable_assembly --keep_standard_contigs INFO 2022-01-25 16:34:31,082...
Hi, I checked the output from metasv, but I find some regions are both duplication and deletion, what caused this？ Scaffold_12628_Chr2 93711 . G . PASS CIEND=-10,10;END=102822;SVLEN=9110;SVTYPE=DUP;CIPOS=-10,10;HOMLEN=2;HOMSEQ=TG;SOURCES=Scaffold_12628_Chr2-93711-Scaffold_12628_Chr2-102819-9108-Manta,Scaffold_12628_Chr2-93711-Scaffold_12628_Chr2-102821-9110-Lumpy,Scaffold_12628_Chr2-93712-Scaffold_12628_Chr2-102822-9110-WHAM;NUM_SVMETHODS=6;NUM_SVTOOLS=3;SVMETHOD=RP,RP,RP,SR,SR,SR;A=15;CF=1.0;CIEND95=0,0;CIPOS95=0,0;CW=0.0,1.0,0.0,0.0,0.0;D=0;DI=0.0;EV=8;I=0;PE=0;SR=7;SS=0;STRANDS=-+:7;SU=7;T=0;TAGS=2931_t4;TF=0;U=15;V=0 GT 0/1 Scaffold_12628_Chr2...
Hi, While running MetaSV, it got errors during the spades process. It seems I can't run the spades successfully, and got nothing finally. Running MetaSV on the same sample with...
I'm trying to set up `metaSV` on a shared HPC on **ComputeCanada**'s [Cedar](https://docs.computecanada.ca/wiki/Cedar) and running into an error with the `pip` installation. Following the [installation instructions](http://bioinform.github.io/metasv/) I download/load the system...
hi, there are some information about "TAGS= sample name" in output vcf file. So, this information tell me which samples have this variantion ? thanks, Kai
Hi there, I have got some vcf files by metasv to merge different tools and assembly. But I don't know how to extract high confidence SNVs from outputs ? could...
Hello, I'm using Lumpy, Breakseq, breakdancer, pindel and cnvnator to look for CNVs in fastq obtained by WES (I know it's not the most adaptable tools for WES). I would...
