I've successfully annotated a VCF file using snpEff but would like to filter the resulting VCF file using snpSift.
The VCF file is in the following format:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 Sample3 A 8725 . C T . PASS ADP=99;WT=2;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/0:145:77:77:77:0:0%:1E0:37:0:41:36:0:0 0/1:0:58:58:55:3:5.17%:9.8E-1:36:33:25:30:3:0 0/0:285:163:162:161:1:0.62%:9.8E-1:36:39:78:83:1:0
I can filter the main columns e.g. INFO column but I don't know how to filter using the "Sample1 Sample2 Sample3" columns by, for instance, only taking vcf entries where one sample has a minimum FREQ of 5% and the other two samples less than 2%.
So far I have this but would like to add the other expressions I detailed above, any ideas how I can do this?
cat A.vcf | java -jar SnpSift.jar filter " ((NC = 0) & ( REF = 'C' ) & ( ALT = 'T')) " > A_filtered.vcf