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Old 05-31-2016, 06:12 AM   #1
AP38
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Default vcftools --minGQ not filtering

Hello,

I am trying to filter based on GQ < 15. I do the following:

vcftools --vcf infile.vcf --minGQ 15 --recode --out filtered

However, this filtering does not work, nothing is being removed: "After filtering, kept 1287174 out of a possible 1287174 Site”. I confirm that the GQ tag is present in my VCF file. Other filters such as min/maxDP or minQ work just fine. I am using VCFtools - v0.1.13

Any thoughts on this would be greatly appreciated.

Thanks!
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Old 06-03-2016, 06:07 AM   #2
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I cross-posted on biostars since I received no answers here:

https://www.biostars.org/p/194918/
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Old 06-03-2016, 06:39 AM   #3
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Previously I tried to use vcftools v0.1.13 to filter my vcf file with --minGQ option, and it worked fine. So it supposed to be some problem with the vcf file than the software. Have you tried to use a different minGO score? which pipeline was used for the vcf generation. I used bowtie2-samtools v0.1.19, and the generated vcf file was good to feed vcftools. hope it helps.
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Old 06-03-2016, 06:49 AM   #4
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Yes, I tried to use a different minGQ, and I had the same issue. The vcf file was created following this workflow:

- samtools mpileup -C 50 -E -t SP -t DP -u -I -f genome -b bam_list.txt > out.bcf
- bcftools call -v -c -f gq out.bcf > out.vcf

Maybe something went wrong with bcftools call?
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Old 06-06-2016, 07:34 AM   #5
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Just posted an answer here:

https://www.biostars.org/p/194918/
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