/fastanno

an ultra-fast tool for annotating flexible tsv files

Primary LanguageGoMIT LicenseMIT

FastAnno : an ultra-fast tool for annotating flexible tsv files

> install or use the binary directly

git clone https://github.com/tsy19900929/fastanno.git
cd fastanno 
go build

> please check tests directory for more details

  • common tsv
fastanno index -f test1_db1.tsv
fastanno anno -q test1_query.tsv -d test1_db1.tsv,test1_db2.tsv -k 1,2 -o test1_out
  • bioinfo vcf
fastanno index -f hg19_AlphaMissense_100.vcf
fastanno anno -q test3_query.vcf -d hg19_AlphaMissense_100.vcf -k 1,2,4,5 -o test3_out
  • vs annovar
    query file test_10000.txt: 10,000 lines, db hg19_AlphaMissense.txt: 69,716,656 lines
    annovar costs 19.2s, fastanno(just use 1 thread) costs 2.6s

> recommend SnpEff + FastAnno as an alternative to ANNOVAR

  • SnpEff is more tiny than VEP, and more HGVS than ANNOVAR
    vs