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tfwillems / HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
GNU General Public License v2.0
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HipSTR not taking the motif lengths > 9 #88

Open think-o opened 1 year ago

think-o commented 1 year ago

Hello,

I have been trying to use HipSTR on the repeat loci, with motif lengths upto 15bp. I get an error for the regions with motif lengths greater than 9bp. The error is something like this:

Region has a PERIOD > 9. Bad line: chr1 54776 54798 10 2 TCCTTTTCTT

Does the tool has a cut off for motif lengths as I cannot find the value for that.

Also, if it is assumed that only STR loci (motif lengths upto 6 bp) should be taken into account, the tool processes the regions bed file with motif lengths upt 8bp. It would be nice if I can get more details on the cut off size for motif lengths.

Thanks, Mali

dinovski commented 1 year ago

Hi Mali, 10-60 bp motifs are considered minisatellites, which is indeed why you're seeing the error. HipSTR does not accept period lengths > 9.