Changes

From Genome Analysis Wiki
Jump to: navigation, search

Vt

324 bytes added, 09:48, 17 June 2015
Filters
Passed Common biallelic SNPs or rare indels : ((PASS&&VTYPE==SNP&&N_ALLELE==2&&INFO.AF>0.005)||(VTYPE&INDEL&&INFO.AF<=0.005))&&QUAL>100
with quality greater than 100
 
Regular expression matching PERL style (implemented with pcre2)
Sometimes, an info field will contain several values in a string with functional annotation, to match what you want,
just use INFO.ANNO=~'<perl regular expression>'
 
Passed variants in intergenic regions : PASS&&INFO.ANNO=~'^Intergenic'
Operations
==,!=,=~,~,&&,||,&,|,+,-,*,/
Failed rare variants : ~PASS&&(INFO.AC/INFO.AN<0.005)
1,102
edits

Navigation menu