Open stroke1989 opened 2 years ago
You can use another variant calling program in theory, but it's a little difficult. After the SNP calling, het_snp_select
step in Accucopy will select the heterozygous SNPs based on the SNP calling results. So, If you use gatk, you should make sure the output of gatk has the same format of Strelka2's output.
The following steps you need to make gatk work in Accucopy:
${strelka_output_dir}/results/variants/variants.vcf.gz
. ${strelka_output_dir}
is default to strelka_snp
, which means the strelka_snp
directory under the folder where the tumor file exists if you don't specify the snp_output_dir
argument. ${strelka_output_dir}
is equal to the snp_output_dir
argument.-s 2
, and the Accucopy will skip SNP_calling
step and use the ${strelka_output_dir}/results/variants/variants.vcf.gz
as the SNPs result directly.Finally, I recommend use Strelka2, because it's easy to use and we have tested it under the impure condition of tumor tissue.
Hi Thanks for this excellent tool. caller_path the path of the 3rd-party variant calling program; in demo, Strelka2 was used. could gatk be uesd as caller?