manta
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Illumina
Structural variant and indel caller for mapped sequencing data
Manta is launched as an LSF command requesting 8 cores. It fails on particular data from 1000 genomes (HG002, HG003, HG004), but works on internal samples. All samples (1000 genomes...
Hi everyone, I am trying to build manta from source by `git clone https://github.com/Illumina/manta`. After making a build directory named `build` and executing `configure`, I executed the following command (I'm...
I successfully detected SV using Manta. When deal with the somaticSV.vcf file using Annovar, i encounter with some error. command line: perl convert2annovar.pl -format vcf4 -allsample -withfreq somaticSV.vcf > sample.annovar...
Hello, Can I run Manta on a GATK realigned and recalibrated BAM or in the original BWA mapped bam? Would the results vary drastically if we ran it on both?...
Hi, we were wondering what are the effects of specifying BED file on variant calling process. Namely we’ve compared two different scenarios - specifying BED file as a method to...
Hi everyone, I am trying to build manta on my macOS 10.15.4 machine, however it failed at building htslib step, here is the build output: > make -C /Users/billy/manta/build ∞...
 Hi, I have an SV that is not being called in the diploidSV.vcf but its seen in the candidateSV, it seems to be failing the diploid model. Any idea...
I am trying run manta on whole genomes and I am getting the following errors: Main fatal error boils down to alignment contains SEQ='*' How do I make sure I...
Hi, team I want to do TestAssembler with few chimeric reads, which support BND, extracted by samtools but do NOT offer reference sequence, Is it any possible? The latest version...
I am repeated getting this error but have';t found any support online, so Does anyone confront such an ERROR while processing?
