Illumina's Manta candidateSmallIndels.vcf.gz Fed Into Illumina's Strelka Using What Sample's candidateSmallIndels.vcf.gz Experimental/Tumor or Normal?

• strelka

  1 342 10.0 C++

  Strelka2 germline and somatic small variant caller (by Illumina)

  

For the Illumina's Strelka code I see something a bit confusing in the somatic configuration example shown below as well as in the url given.

• manta

  3 363 0.0 C++

  Discontinued Structural variant and indel caller for mapped sequencing data (by Illumina)

  

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?

• InfluxDB

  www.influxdata.com sponsored

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

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