Graph Mapper Hash Table Options

The following are additional ALT-aware file options to control building hash tables for the DRAGEN graph mapper.

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--ht-pop-alt-contigs —Specifies the path to the reference FASTA file with population alternate contigs. The standard reference FASTA is augmented with the population alternate contigs during hash table build. The population alternate contigs file must have a corresponding liftover SAM file. A population alternate contig file for hg38 reference is provided in /opt/edico/liftover (pop_altContig.fa.gz).

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--ht-pop-alt-liftover—Specifies the path to the liftover file for the population alternate contigs. The liftover SAM file must have a corresponding population alternate contigs FASTA. A population alternate contig SAM liftover file for hg38 reference is provided in /opt/edico/liftover (pop_liftover.sam.gz).

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--ht-pop-snps—Specifies the path to a VCF file containing unphased population SNPs. The standard reference FASTA is augmented with these SNPs as multibase codes during mapping-aligning. Each SNP entry in the VCF only requires the CHROM, POS, REF, ALT columns. The ALT column can have multiple comma-separated population SNP VCF for hg38 reference is provided in /opt/edico/liftover (pop_snps.vcf.gz).