Filter field are all ".", no "PASS" in vcf file ?
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6.6 years ago
897598644 ▴ 100

I have used HaplotypeCaller to call variants in a whole exome sequencing data.When I scan the file, i found in the Filter field all are ".",even no "PASS",but most of the sites have high QUAL. Why?

thx in advance

software error next-gen sequencing genome • 2.1k views
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Just double checking, are you sure it's the FILTER field and not the ID field you're looking at?

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I know it's a pretty old post but I am seeing the same thing in my VCF file (btw data is also pretty old like 6-7 years)

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