Add "-l 100" flag to the paftools.js call command in the call_variants.sh script to allow for smaller genome sizes

[molly-hetheringtonrauth]

Hi!

I'm using your pipeline for the influenza HA segment which is only 1.7kb long. Without the "-l 100" flag added in addition to the currently used "-L 100" to the paftools.js call subcommand, all alignments will be dropped and no variants called because the default alignment length is 10kb. Adding this flag would not affect the pipeline for covid because covid is 30kb.

The new command would look like this:

minimap2 -c -x asm20 --end-bonus 100 -t 20 --cs $single_ref_path $fasta 2>${fasta%.fa}.paftools.log | sort -k6,6 -k8,8n > ${fasta%.fa}.paf && paftools.js call -s ${fasta%.fa} -L 100 -l -f $single_ref_path ${fasta%.fa}.paf > ${fasta%.fa}.vcf 2>>${fasta%.fa}.paftools.log;

See https://github.com/lh3/minimap2/blob/master/misc/README.md for the paftools.js documentation on this.

I've currently just modified the code on the script I've pulled from your repo but this may be a helpful change for other users as well.

Thanks!