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problem to filter freq from vcf produced with varscan

I have a VCF file obtained from the Varscan2 tool. I want to filter the variants based on "FREQ". I used SnpSift (SnpSiftVersion="SnpSift 4.2 (build 2015-12-05), by Pablo Cingolani"). When I used the command: java -Xmx64g -jar ${SNPSIFT_JAR} extractFields $svcf "GEN[1].FREQ" I got the right field of my vcf file: 0.52% 0% 0.72% 0% 0.31% 0.21% 0.31% 0.31%

But when I tried to filter variant with a freq greter than 0.1, no variant pass the filter. I ran this command: java -Xmx64g -jar ${SNPSIFT_JAR} filter " ( GEN[0].FREQ > 0.1 ) " $svcf

I got the feeling that freq is not an integer.

Any suggstion?

thank you Marco

varscan2 filter vcf snpsift
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written by fabbri.marco • fabbri.marco

1 answer

from this old file https://github.com/blachlylab/mucor/blob/master/examples_package/data/NA12878.VarScan.indels.vcf (2015)

FREQ is a string

##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">

check this in your VCF header.

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written by Pierre Lindenbaum Pierre Lindenbaum

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