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, 10:29, 17 June 2015
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| 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 |
| + | Failed rare variants : ~PASS&&(INFO.AC/INFO.AN<0.005) |
| | | |
| Regular expression matching PERL style (implemented with pcre2) | | Regular expression matching PERL style (implemented with pcre2) |
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| just use INFO.ANNO=~'<perl regular expression>' | | just use INFO.ANNO=~'<perl regular expression>' |
| | | |
− | Passed variants in intergenic regions : PASS&&INFO.ANNO=~'^Intergenic' | + | Passed variants in intergenic regions or UTR : PASS&&INFO.ANNO=~'Intergenic|UTR' |
| | | |
| + | |
| Operations | | Operations |
− | ==,!=,=~,~,&&,||,&,|,+,-,*,/
| + | ==,!=,=~,~,&&,||,&,|,+,-,*,/ |
− | | + | |
− | Failed rare variants : ~PASS&&(INFO.AC/INFO.AN<0.005) | |
− | | |
| The motivation in this case is because Indels are a heterogeneous set of variants and thus we usually examine them | | The motivation in this case is because Indels are a heterogeneous set of variants and thus we usually examine them |
| from many different characteristics. The following programs support filter support. | | from many different characteristics. The following programs support filter support. |