http://statgen.us/index.php?action=history&feed=atom&title=Functional_Annotation_Exercise 2026-04-05T19:45:37Z Revision history for this page on the wiki MediaWiki 1.26.2 http://statgen.us/index.php?title=Functional_Annotation_Exercise&diff=754&oldid=prev 2019-01-24T18:31:28Z

<p>Created page with &quot;__NOTITLE__ ==Functional Annotation Exercise== &lt;pre&gt;table_annovar.pl table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Gene.vcf -remove -nastring . -protocol ref...&quot;</p> <p><b>New page</b></p><div>__NOTITLE__<br /> <br /> ==Functional Annotation Exercise==<br /> <br /> &lt;pre&gt;table_annovar.pl<br /> table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Gene.vcf -remove -nastring . -protocol refGene -operation g -vcfinput<br /> cat APOC3_Gene.vcf.hg19_multianno.txt<br /> table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Gene.vcf -remove -nastring . -protocol refGene,knownGene,ensGene -operation g,g,g -arg '-splicing 12 -exonicsplicing','-splicing 12 -exonicsplicing','-splicing 12 -exonicsplicing' -vcfinput<br /> awk -F'\t' '{print $1,$2,$6,$7,$8,$9,$10}' APOC3_Gene.vcf.hg19_multianno.txt<br /> table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Region.vcf -remove -nastring . -protocol phastConsElements46way -operation r -vcfinput<br /> table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Region.vcf -remove -nastring . -protocol gwasCatalog -operation r -vcfinput<br /> table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_Filter.vcf -remove -nastring . -protocol gnomad_genome,gnomad_exome,popfreq_max_20150413,gme,avsnp150,dbnsfp33a,dbscsnv11,cadd13gt20,clinvar_20170905,gwava -operation f,f,f,f,f,f,f,f,f,f -vcfinput<br /> awk -F'\t' '{print $1,$2,$103,$104}' APOC3_Filter.vcf.hg19_multianno.txt<br /> awk -F'\t' '{print $1,$2,$6,$14}' APOC3_Filter.vcf.hg19_multianno.txt<br /> awk -F'\t' '{print $1,$2,$15,$16,$17,$18,$19,$20,$21,$22}' APOC3_Filter.vcf.hg19_multianno.txt<br /> awk -F'\t' '{print $1,$2,$36,$86,$70}' APOC3_Filter.vcf.hg19_multianno.txt<br /> awk -F'\t' '{print $1,$2,$99,$100}' APOC3_Filter.vcf.hg19_multianno.txt<br /> table_annovar.pl APOC3.vcf humandb/ -buildver hg19 -out APOC3_ANN.vcf -remove -nastring . -protocol refGene,knownGene,ensGene,wgRna,targetScanS,phastConsElements46way,tfbsConsSites,gwasCatalog,gnomad_genome,gnomad_exome,popfreq_max_20150413,gme,avsnp150,dbnsfp33a,dbscsnv11,cadd13gt20,clinvar_20170905,gwava -operation g,g,g,r,r,r,r,r,f,f,f,f,f,f,f,f,f,f -arg '-splicing 12 -exonicsplicing','-splicing 12 -exonicsplicing','-splicing 12 -exonicsplicing',,,,,,,,,,,,,,, -vcfinput<br /> &lt;/pre&gt;</div>

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