Evie Wan

Integrated Sniffles2 to CallVariantsPBCCS.wdl. Test ran on sample HG00514. Sniffles2 will call variants across the whole genome only since the .snf files can't be merged.

In this PR, I added a workflow "MitochondriaProcessing" to call variants from mitochondrial reads. In this workflow, I subset chrM reads from bam file and used Hifiasm and Minimap2 for...

Trivial bug fix for paftools.js call - adding `-L10000`.

Workflow filters contigs of the right lengths, identifies overlapping regions, and eventually selects contigs that represent the major haplotype based on the number of SNPs.

add optional input parameter length_threshold for paftools.js call

1

Added an optional parameter length_threshold. From minimap2 Github page: "paftools.js call ignores alignments 50kb or shorter; when deriving callable regions, it ignores alignments 10kb or shorter". For mitochondria variant calling,...

updated Dockerfile and Makefile for Canu2.2 version update. added "technology" parameter in Canu.wdl to specify nanopore vs pacbio sequencing method