Question: filtered and dropped vcfs empty when filtering 1000 gemomes variants with Annova
0
gravatar for ekwame
3 months ago by
ekwame60
NYC
ekwame60 wrote:

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

ADD COMMENTlink modified 3 months ago • written 3 months ago by ekwame60
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