From Genome Analysis Wiki
Jump to navigationJump to search
324 bytes added
, 09:48, 17 June 2015
Line 109: |
Line 109: |
| 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 | | 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 | | 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 | | Operations |
− | ==,~,&&,||,&,|,+,-,*,/ | + | ==,!=,=~,~,&&,||,&,|,+,-,*,/ |
| | | |
| Failed rare variants : ~PASS&&(INFO.AC/INFO.AN<0.005) | | Failed rare variants : ~PASS&&(INFO.AC/INFO.AN<0.005) |