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mehrdadbakhtiari / adVNTR

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
http://advntr.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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subset hg19_genic_VNTRs.db #43

Closed psychrb closed 2 years ago

psychrb commented 3 years ago

Can you please clarify advise? For genotyping a specific subset of VNTRs from the n=158,522 VNTRs loci (i.e. a subset of the hg19_genic_VNTRs.db within vntr_data_genic_loci.zip): 1) Can the VNTRs be subsetted by specific VNTRs of interest within, if I specify chromosome and coordinates?? 2) This input code could then just include this subsetted reference file...correct? advntr genotype -m vntr_data subsettedfile.db -f filename.bam --working_directory ./ -of vcf -o filename_advntr.vcf Thanks.

Jong-hun-Park commented 3 years ago

Yes, you can use a customized set of reference VNTRs. If you selected a subset of vntr_data_genic_loci.zip, it should work.