Hi
I'm using annovar to filter germline variants by --score_threshold but nothing is either filtered or dropped.
please I'm I missing something in the code?
perl annotate_variation.pl --filter /sc/hydra/projects/canan/Breast_Cancer/results/germline/new_germline07302020/Germline_108_07302020.vcf.gz
./ --vcfdbfile humandb/1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf --dbtype vcf --buildver hg38
--outfile cuimc_1000g_filtering_all --score_threshold 0.001
NOTICE: Output file with variants matching filtering criteria is written to cuimc_1000g_filtering_all.hg38_vcf_dropped, and output file with other variants is written to cuimc_1000g_filtering_all.hg38_vcf_filtered NOTICE: Variants with invalid input format are written to cuimc_1000g_filtering_all.invalid_input
files produced
(base) [ahunos01@lc02a27 exercise1]$ ls -thl
total 11G
-rw-r----- 1 ahunos01 canan 910 Aug 7 09:57 cuimc_1000g_filtering_all.log
-rw-r----- 1 ahunos01 canan 620M Aug 7 09:57 cuimc_1000g_filtering_all.invalid_input
-rw-r----- 1 ahunos01 canan 0 Aug 7 09:57 cuimc_1000g_filtering_all.hg38_vcf_dropped
-rw-r----- 1 ahunos01 canan 0 Aug 7 09:57 cuimc_1000g_filtering_all.hg38_vcf_filtered
triied specifying vcfinput but i get syntax error
(base) [ahunos01@lc02a27 exercise1]$ perl annotate_variation.pl --filter /sc/hydra/projects/canan/Breast_Cancer/results/germline/new_germline07302020/Germline_108_07302020.vcf.gz ./ --vcfdbfile humandb/1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf --dbtype vcf --buildver hg38 --outfile cuimc_1000g_filtering_all --score_threshold 0.001 --vcfinput
Unknown option: vcfinput
Usage:
annotate_variation.pl [arguments] <query-file|table-name> <database-location>
annovar version is
Version: $Date: 2020-06-07 23:56:37 -0400 (Sun, 7 Jun 2020) $
thanks for your help Sam
