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StructuralVariationDiscoveryPipelineSpark Documentation

The StructuralVariationDiscoveryPipelineSpark requires the parameter --contig-sam-file.

However, there is no description of the parameter in the input and the example code.


  • An input file of aligned reads.
  • The reference to which the reads have been aligned.
  • A BWA index image for the reference. You can use BwaMemIndexImageCreator to create the index image file.
  • A list of ubiquitous kmers to ignore. You can use FindBadGenomicGenomicKmersSpark to create the list of kmers to ignore.

Usage example
gatk StructuralVariationDiscoveryPipelineSpark \
-I input_reads.bam \
-R reference.2bit \
--aligner-index-image reference.img \
--kmers-to-ignore ignored_kmers.txt \
-O structural_variants.vcf

In the parameter listing, there is this.

--contig-sam-file sam file for aligned contigs

Could more details on this parameter be made available? How is the file generated and its format/contents?

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    Unfortunately, since the tool is still in beta, we don't have much more documentation. I will see if I can find out more about the --contig-sam-file for you.


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