how to filter based on FREQ from snpsift annotation for vcf files?
After annotating by snpsift, how could I filter based on FREQ?
For example, a record with the following annotation, and I would like to filter based on GnomAD. How should I write the expression? Many thanks!
Note there are four value, the first is the ref with frequency of 0.3163, and the alt represented in the record has a freq of 0.6837. "." means other variants are not found for this sample.
FREQ=GENOME_DK:0.05556,.,0.9444,.|GnomAD:0.3163,.,0.6837,.|KOREAN:0.1405,0,0.8595,0|SGDP_PRJ:0.0181,0.002262,0.9751,0.004525|TOMMO:0.1327,.,0.8673,.|dbGaP_PopFreq:0.0779,.,0.9221,.
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What have you tried? Did you google "filter VCF based on INFO attribute"?
Yes, I have tried. In the documentation of snpsift filter, the expression for INFO fields other than ANN are not clear. And I am not sure how to deal with "." in the annotation of "GnomAD:0.3163,.,0.6837,.".
Look at other, more basic ways of filtering VCF files.
bcftools view might be helpful, but do you have more specific ideas how to filter the FREQ field, it looks quite complicated to me.
Yes - that's what you need. Look at
includeexpressions.