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Manta cannot detect same chromosome large deletions

7

Hi, I generated test cases and was trying to detect large deletions within the same chromosomes and found that manta wasn't calling them. Viewing in IGV the gaps are visible....

jdzdroid

Permission Denied Error with convertInversion.py

2

I've tried to install this on (a) our research cluster, (b) inside a Singularity container, and (c) on my Macbook. All of these methods produce a similar error. I've tried...

mdbjax

[Question]: Is ARM64 architecture supported ?

1

Hi, I'd like to ask whether it is OK to run Manta on Linux/MacOS ARM64 machines ? Thank you!

julien-faye

Versioning on conda

1

Hello, I would like to ask about the latest release on conda (manta version 1.6.0 released on May, 21 2022, tar file name: manta-1.6.0-h9ee0642_2.tar.bz2). I see that it is labeled...

dmaziec

Filter bad-cigar reads in bam streamer

1

These reads are ok according to SAM/BAM spec, but Manta can't work with them. This fixes issue https://github.com/Illumina/manta/issues/137 "Manta crashes on input files realigned with ABRA #137" as well as...

fbattke

Failed to complete command task: 'getAlignmentStats_generateStats_000'

3

I am running manta 1.6.0 with alignment output from STAR-Fusion's Aligned.out.sam after it is compressed to bam and sorted. The manta options for the configManta.py I used was `--rna --bam...

zetamui

[ERROR] Failed to complete command task: 'generateCandidateSV_0000' with taskExitCode -9

3

Hi, I'm running manta-1.6.0 for days and an error came out, I have no idea of how to solve it. Can anyone help me? ``` [2021-10-18T05:27:26.963507Z] [cngb-compute-e03-8.cngb.sz.hpc] [90379_1] [TaskRunner:generateCandidateSV_0000] Task...

Mirror-fish

Hi Matainer ✋ ! I really appreciate the maintenance of the tool, and I have a question about the orientations of structural variation. For example, could we know the orientation...

cauliyang

Split and spanning reads

1

Hello, In the VCF file, tags for spanning and split reads store the information about the support for the alternative and reference alleles. ``` ##FORMAT= ##FORMAT= ``` Could you explain...

dmaziec

Fail to open existing file

2

Hi, manta is returning an error that cannot open a file (that exists), but that I think might relate to the number of samples used, or probably something else. When...

elcortegano