use T2T-CHM13 as reference

maiziezhoulab / VolcanoSV

VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing

MIT License

5 stars 0 forks source link

use T2T-CHM13 as reference #8

Closed DayTimeMouse closed 4 weeks ago

DayTimeMouse commented 4 weeks ago

Hi,

I'd like to use T2T-CHM13 as reference, how to set -rv?

python3 ${path_to_volcanosv}/bin/VolcanoSV-vc/Small_INDEL/volcanosv-vc-small-indel.py \
-i volcanosv_asm_output/ \
-o volcanosv_small_indel \
-bam Hifi_L2_hg19_minimap2_chr10.bam \
-ref refdata-hg19-2.1.0/fasta/genome.fa \
-rv 37 \
-r chr10 \
-t 30 \
-px Hifi_L2

Best regards.

volcano1998 commented 4 weeks ago

Thank you for pointing it out! I further checked this detail and realized the reference version doesn't matter. I just removed this flag and updated the readme.