Run

Single sample

Extract informative pairs to a binary format

strling extract -f $reference_fasta /path/to/$name.cram $name.bin

Call strs on the extract binary data

mkdir -p str-results/
strling call --output-prefix str-results/$name -f $reference_fasta /path/to/$name.cram $name.bin

Joint calling

Extract informative pairs to a binary format for a single sample (same as above)

strling extract -f $reference_fasta /path/to/$sample2.cram $sample1.bin
strling extract -f $reference_fasta /path/to/$sample2.cram $sample2.bin

Joint call call str loci accross all samples

mkdir -p str-results/
strling merge --output-prefix str-results/joint -f $reference_fasta $sample1.bin $sample2.nim

Call strs on a single sample

strling call --output-prefix str-results/$sample1 -b str-results/joint-bounds.txt -f $reference_fasta /path/to/$sample1.cram $sample1.bin
strling call --output-prefix str-results/$sample2 -b str-results/joint-bounds.txt -f $reference_fasta /path/to/$sample2.cram $sample2.bin