Manta SV Caller

DNAnexus platform implementation of Illumina's Manta structural variant caller. Can perform single sample or paired analysis.

See the Manta User Guide (https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md) for details on Manta.

Inputs

normal_bam (Required): One or more germline BAM files. Required for either germline only or paired analysis. If paired, only the first file will be used.
normal_bam_index: Index file(s) for germline BAM files. If none are provided, the app will generate them.
tumor_bam: Tumor BAM file. If provided, app will assume tumor normal analysis.
tumor_bam_index: Tumor BAM index file. If one is not provided, the app will generate it.
reference_fasta (Required): Reference FASTA file. If not provided, a default hg38 reference FASTA will be used. If running hg19 samples, this input is required or the app will error.
reference_fasta_index: Reference FASTA file index. If not provided, an index will be generated.
output_contig: Boolean flag for the 'outputContig' option on manta. [default: true]
call_regions: Boolean flag for the 'callRegions' option on manta. Only works on hg38 samples. [default: true]
output_prefix: Prefix to add to output files.

Outputs

variant_outputs: Outputs under the 'variant' folder. It includes: candidateSV.vcf.gz candidateSV.vcf.gz.tbi diploidSV.vcf.gz diploidSV.vcf.gz.tbi candidateSmallIndels.vcf.gz candidateSmallIndels.vcf.gz.tbi somaticSV.vcf.gz somaticSV.vcf.gz.tbi
statistics_outputs: Outputs under the 'statistics' folder. alignmentStatsSummary.txt svLocusGraphStats.tsv svCandidateGenerationStats.xml svCandidateGenerationStats.tsv

Tips

Instance Types - Manta can parallelize across multiple cores, therefore it is preferable to choose an instance type with many cores. The other key factor in determining instance type is the storage required to store all the input and reference files. We recommend mem1_ssd1_x16 or bigger instances.
Runtime - To reduce runtime and costs, make sure to include a reference FASTA file and all index files. The app will need the input files to be indexed before running.
Hg19 samples - To run hg19 samples, specify the reference_fasta and reference_fasta_index inputs as the default references are GRCh38. Call Regions option should be set to false.

Troubleshooting

Storage

Ensure the instance type has enough storage space for all the inputs and reference files. The reference fasta is about 3GB in size.

Typically for single WGS germline analysis, we recommend azure:mem1_ssd1_x8 or azure:mem1_ssd1_x16 instances. For tumor-normal paired analysis, we recommend azure:mem2_ssd1_x16.

Input mismatches

If the index files are not correct or if the germline, tumor samples aren't a pair, then the app will error possibly with a vague error message. If the app has errors where it cannot read the input bams, ensure that all the indices are correct. It is also recommended to input the correct reference FASTA to the app.

stjudecloud / dx-manta