Shulou(Shulou.com)06/01 Report--

This article mainly introduces how to use the ANNOVAR annotation of HGMD human variation database. The introduction in this article is very detailed and has certain reference value. Interested friends must read it!

HGMD Human Variation Database ANNOVAR Annotations Use

Official instructions: resources.qiagenbioinformatics.com/tech-notes/HGMD_Tech_Note.pdf

But we need to convert it so that ANNOVAR can support vcf batch annotation. The perl script is converted as follows:

perl ./ prepare_hgmd.pl HGMD_PRO_2016.4_hg19.vcf hg19_HGMD_PRO_2016.4.txtmy ($dbfile) = $ARGV[0];my ($outfile) = $ARGV[1];open (FH, "perl /share/work/biosoft/annovar/2018Apr16/annovar/convert2annovar.pl -format vcf4 -include $dbfile |") or die "Error: cannot read from dbfile $dbfile: $!\ n";if ($outfile) {open (OUT, ">$outfile") or die "Error: cannot write to output file: $!\ n";print OUT "#Chr\tStart\tEnd\tRef\tAlt\tHGMD\n";}while () {m/^#/ and next; s/[\r\n]+$//;my @field = split(/\t/, $_);my$HGMD="HGMDID=$field[7];";my$info="$HGMD$field[12]";#$info=~ s/;/\\x3b/g;#$info =~ s/,/\\x2c/g;#$info=~ s/=/\\x3d/g;print OUT join ("\t", @field[0.. 4], $info), "\n";}close OUT; The above is "HGMD human variation database ANNOVAR comments how to use" All the content of this article, thank you for reading! Hope to share the content to help everyone, more relevant knowledge, welcome to pay attention to the industry information channel!

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.