gravatar for BAGeno

2 hours ago by

Hi,

I am using bcftools filter. I run bcftools filter command in two different ways. It gave me different results.

Command #1

 bcftools filter --e "GQ<20" miss.GT.vcf.gz>test1.vcf

This gave me 49336 variants.

while when I run command 2

 bcftools filter -i "GQ>20" miss.GT.vcf.gz>test2.vcf

It gave me 80858 variants.

There are 80858 variants in original file.

Why there is such variation? Which command results should I consider for further analysis?

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modified 1 hour ago

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2 hours ago
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BAGeno170



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