Tandem Repeat Benchmark Variant Representation

[TimD1]

I'm trying to figure out which Smith-Waterman parameters were used to select the representation of variants in the tandem repeat ground truth VCF.

From my understanding, this line in variants/scripts/map_haplo.sh uses minimap2 to align each haplotype to the reference FASTA, therefore selecting the variant representation.

My confusion arises from the fact that params='-x asm20 ... -O 5,56 -E 4,1 -B' in this line. Based on the minimap2 documentation, if you want to override the mismatch penalty, you must provide -B INT. For me, not providing this value results in [ERROR] missing option argument. Are you overriding the mismatch penalty? If so, with what value? If not, then what does the -B flag do here?

Thanks in advance for clarifying!

[ACEnglish]

The value of -B 5 was supposed to there. Looks like the line in the code got erroneously truncated. Minimap2.24 was used for the initial alignments and it does not throw an error with only -B. Looking at the logs from the benchmark's alignment I believe the truncated line was used so presumably -B 4 (minimap's default) was used.

[TimD1]

Thanks for the quick response!