The StructuralVariationDiscoveryPipelineSpark requires the parameter --contig-sam-file.
However, there is no description of the parameter in the input and the example code.
Inputs
- 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?