manta SV is generating no output files

usegalaxy.eu support
, ,
1

Hello, I am investigating tools for structural variant screening of illumina sequencing data sets in fungi. I tested Manta, and it “runs” but the first attempt produced a config file, and nothing else (such as the set of VCF 4.1 files mentioned as output). I tried switching versions of the software, and the second produced nothing at all, and the screen upon submission listed no files generated. I’m using a BWA-MEM2 .bam file as input as ‘normal’, and a reference genome .fasta, intending to have the program build an index.

am I meant to use the contig file for a local downloaded instance of manta? Are the VCF files just not being generated?

Thanks for any help on this.

config file was as below. >

"#

This section contains all configuration settings for the top-level manta workflow,

[manta]

referenceFasta = /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa

Run discovery and candidate reporting for all SVs/indels at or above this size

Separate option (to provide different default) used for runs in RNA-mode

minCandidateVariantSize = 8
rnaMinCandidateVariantSize = 1000

Remove all edges from the graph unless they’re supported by this many ‘observations’.

Note that one supporting read pair or split read usually equals one observation, but evidence is sometimes downweighted.

minEdgeObservations = 3

If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge.

Set to 0 to turn this filtration off

graphNodeMaxEdgeCount = 10

Run discovery and candidate reporting for all SVs/indels with at least this

many spanning support observations

minCandidateSpanningCount = 3

After candidate identification, only score and report SVs/indels at or above this size:

minScoredVariantSize = 50

minimum VCF “QUAL” score for a variant to be included in the diploid vcf:

minDiploidVariantScore = 10

VCF “QUAL” score below which a variant is marked as filtered in the diploid vcf:

minPassDiploidVariantScore = 20

minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf:

minPassDiploidGTScore = 15

somatic quality scores below this level are not included in the somatic vcf:

minSomaticScore = 10

somatic quality scores below this level are filtered in the somatic vcf:

minPassSomaticScore = 30

Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote

locations with poor mapping quality, which pair to confidently mapping reads near the insertion locus. These reads

can help to fully assemble longer insertions, under certain circumstances this feature can add a very large runtime

burden. For instance, given the very high chimeric pair rates found in degraded FFPE samples, the runtime of the read

retrieval process can be unpredicable. For this reason the feature is disabled by default for somatic variant calling.

This feature can be enabled/disabled separately for germline and cancer calling below.

Here “CancerCallingModes” includes tumor-normal subtraction and tumor-only calling. “GermlineCallingModes” includes

all other calling modes.

enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1
enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0

Set if an overlapping read pair will be considered as evidence

Set to 0 to skip overlapping read pairs

useOverlapPairEvidence = 0"

2

Hi @Erin_Bredeweg

Yes, you might need to toggle some of the form parameters.

For example, this one will output an additional VCF compared to the defaults.

Unfiltered small indel candidates

I have a test history here that you are welcome to copy or explore: https://usegalaxy.eu/u/jenj/h/test-manta

Small note: to get a VCF file that other tools can interpret, click on the pencil icon to reach the convert tools.

Please let us know is this helps or not! You are also welcome to share your history for more specific feedback since sometimes the formats of the input files can matter and we can help to confirm. See the banner at this forum or here directly to learn how to generate a share link. You can paste that back here. → How to get faster help with your question :slight_smile: