Nirvana
The nimble & robust variant annotator (by Illumina)
manta
Structural variant and indel caller for mapped sequencing data (by Illumina)
| Nirvana | manta | |
|---|---|---|
| 1 | 3 | |
| 166 | 363 | |
| 0.6% | - | |
| 3.6 | 0.0 | |
| about 2 months ago | over 1 year ago | |
| C# | C++ | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 only |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Nirvana
Posts with mentions or reviews of Nirvana.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-23.
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What to do with Manta outputs
I think I am already stressed out by it but I have processed a lot data with Manta and I kind of need the results so you as saying Illumina's Manta can be fed into Illumina's Nirvana (https://github.com/Illumina/Nirvana)? Have you used it with Manta before?
manta
Posts with mentions or reviews of manta.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-06-20.
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Illumina's Manta candidateSmallIndels.vcf.gz Fed Into Illumina's Strelka Using What Sample's candidateSmallIndels.vcf.gz Experimental/Tumor or Normal?
It says it uses the `candidateSmallIndels.vcf.gz` created by Illumina's Manta however, I cannot seem to find information as to if this `candidateSmallIndels.vcf.gz` is created by Manta using the tumor bam or the normal. Does anyone perchance know which sample was used in creation of the `candidateSmallIndels.vcf.gz` used here? As `candidateSmallIndels.vcf.gz` seems to be made per sample from what I understand of Illumina Manta's documentation?
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What to do with Manta outputs
I am looking at the Manta structural variant caller https://github.com/Illumina/manta. I successfully got it to work however, I am unsure of how to process the outputs further. I am particularly interested in the `diploidSV.vcf.gz` file but when I try to process it through ANNOVAR it doesn't work. What should I do to process this output further?
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Manta & denovo_scoring.py & How To Write The Code?
I am trying to use `denovo_scoring.py` in Manta ( https://github.com/Illumina/manta ) but I cannot seem to figure out the code. What should I use?
What are some alternatives?
When comparing Nirvana and manta you can also consider the following projects:
strelka - Strelka2 germline and somatic small variant caller
Sniffles - Structural variation caller using third generation sequencing
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)