metasv

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Hi, I'm trying ti use MetaSV for the first time. I installed version 0.5.2. I checked that reference.fa and reference.fa.fai are in the same folder with excatly the same name....

fabfabBesnard

How to include SV calls from Delly

9

Hi Marghoob, I’m interested to use MetaSV for identifying high confidence SVs from 3 different algorithms e.g. BreakDancer, Delly and CNVnator. I was wondering whether it is possible to include...

MMesbahU

IOError: [Errno 2] No such file or directory: 'cnvnator.call'

3

Hi, I installed metasv using pip install and when I run it I get a missing file cnvnator.call. Full log is below signature. Thanks, Colin run_metasv.py --reference /wd5/sq/grch37decoy/hs37d5.000.fa --breakdancer_native breakdancer.out...

colinhercus

type 'exceptions.IOError': Broken pipe

2

Hi, I'm running metaSV with cmd like: `run_metasv.py --reference /home/gst/work/ref/Zea_mays.AGPv4.dna.toplevel.fa --boost_sc --pindel_vcf Q417_pindel.vcf --breakdancer_vcf Q417_breakdancer.vcf --cnvnator_native Q417_cnvnator.out --manta_vcf Q417_manta.vcf --lumpy_vcf Q417_lumpy.vcf --wham_vcf Q417_whamg.vcf --mean_read_length 150 --sample Q417 --bam /home/gst/work/b73_BWAMEM_bam/Q417_bwa/Q417.bwamem.sort.bam --spades...

songtaogui

Memory error when using metasv

9

I'm using metasv to merge the output of pindel, cnvnator and breakdancer. But I get the error "OSError: [Errno 12] Cannot allocate memory". I want to know if the metasv...

daxian248

Error while reading AGE output

3

Hi, I am using Meta-SV version 0.5.4. I got an error while reading the Age output. I am attaching the error file here. It would be great if you can...

jasjitbanwait

Hello, It seems to be great tool for merging SV calls from multiple tools. I did a quick run with provided script "run_test.sh" as well as with our data from...

npatel22526

I as wondering if MetaSV does "joint genotyping" of multiple samples, analogous to what GATK does for SNPs? Does MetaSV do break-point resolution? For example, if I have a population...

ldorozco

Insertion detection

3

Hello, When I try to run enhanced insertion detection, I get an error message. This is my command: run_metasv.py --reference /mnt/data/GRCh37_bcgsc/GRCh37-lite.fa --boost_sc --sample A48018 --bam /mnt/data/A48018_2_lanes_dupsFlagged.bam --spades /home/hpcuser01/SPAdes-3.6.2-Linux/spades.py --age /home/hpcuser01/AGE/age_align...

Madelinehazel

This is the attempt to integrate softclip stand-alone calls to MetaSv. Please don't merge yet.

msahraeian