simple repeat filtered result is not included in vcf output

[charliechen912ilovbash]

Hello, I am using version 0.7.0. Is there any way to filter the vcf output with post_filter.py ?

[friend1ws]

Thanks! Could you check the tutorial page? https://github.com/friend1ws/nanomonsv/wiki/Tutorial#removing-indels-within-simple-repeat It should work fine.

[charliechen912ilovbash]

Excuse me, I mean to filter the "VCF" file, not the SV list file.

[friend1ws]

Sorry for the delay. You may be able to use the function in nanomonsv

First, prepare the following scripts and name it as, e.g., nanomonsv_converter.py

#! /usr/bin/env python3

import sys
from nanomonsv.vcf_convert import genomesv2vcf_convert

genomesv2vcf_convert(sys.argv[1], sys.argv[2], sys.argv[3])

Then try the command as:

$ python3 nanomonsv_converter.py COLO829.nanomonsv.result.txt COLO829.nanomonsv.result.vcf ${reference_genome_path}

[charliechen912ilovbash]

I understood, thanks for reply.