metasv
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bioinform
MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
I added the option to incorporate delly vcf files. Had a couple question to go along with my changes noticed when i changed metasv locally the changes wouldn't go into...
It looks like metaSV ignores translocations in Lumpy vcf files. When I run metaSV, I get these messages ( a short sample): INFO 2016-10-28 11:30:02,622 metasv.main Load VCF files INFO...
I am running Metasv with local assembly for duplication variants. My input is only 5 duplication variants and 4 of them were skipped due to small size, so there is...
Hello, There seems to be some bug in metaSV when the --boost_scs option is included. With this option, my deletion detection sensitivity drops dramatically from ~80% to 5% (as measured...
Hello, I've run MetaSV and received this following message: --- ERROR 2016-02-23 02:20:01,971 run_spades_single- Caught exception in worker thread Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/metasv/run_spades.py", line 75, in run_spades_single...
Hello, I ran: python2.7 run_metasv.py --version run_metasv.py 0.5 module load bedtools/2.24.0 module load gcc/4.8.4 PATH=$PATH:/bcbiometasv/miniconda/bin PYTHONPATH="${PYTHONPATH}:/bcbiometasv/miniconda:/bcbiometasv/miniconda/lib/python2.7/site-packages" python2.7 run_metasv.py --reference hg19_chromosome.fa --boost_sc \ --age /bcbiometasv/miniconda/bin/AGE-master/age_align \ --pindel_vcf 5.realigned.pindelx5_1toY.N0_PTonly_LI.filtered.somatic.142.recode.vcf 6.realigned.pindelx5_1toY_N0.PTonly_TD.filtered.somatic.142.recode.vcf 7.realigned.pindelx5_1toY_N0.PTonly_D.filtered.somatic.142.recode.vcf 8.realigned.pindelx5_1toY_N0.PTonly_INV.filtered.somatic.142.recode.vcf...
the Makefile for the custom version of age_align has -O3 option added, on my debian systems at least this pretty well breaks age_align. it hangs most of the time, even...
Hi there, Reading the metaSV [paper](http://bioinformatics.oxfordjournals.org/content/early/2015/04/10/bioinformatics.btv204.full.pdf). I am interested in how do you implement the "Merge overlapping calls per tool (intra-tool merging)" I have read a post on bedtools google...
Hello, can you please add description of the output for metasv explaining all the flags in the vcf. This will help to further filter the metasv results.
