Using Biopet VcfFilter

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3.8 years ago

Domu • 0

Hey, I heard one can use the Biopet VcfFilter to filter out reference calls from our sample calls. Can someone tell me how this is done?

Thanks in advance!

snp • 705 views

ADD COMMENT • link 3.8 years ago by Domu • 0

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Do you mean filter out 0/0 calls? Does the solution need to use biopet/vcffilter? Other more popular tools such as bcftools could have this capability too.

ADD REPLY • link 3.8 years ago by Ram 43k

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I have a set of variants in a separate vcf files which needs to be removed from variants in a second vcf file. This doesn't necessarily need VcfFilter, any software which can do that is fine

ADD REPLY • link 3.8 years ago by Domu • 0

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Read the bcftools manual. bcftools view -R vcf_file should probably do the trick.

ADD REPLY • link 3.8 years ago by Ram 43k

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I checked the manual and I think the -R has been replaced by the -V. However, the variant is only excluded if the ALT matches between the two, in my case it is likely that the ALT might not match because of sequencing errors. In that case the variant might not be excluded. Is there a position based filtering option?

ADD REPLY • link 3.8 years ago by Domu • 0

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-R has been replaced by -V

Sorry, what? No it has not been replaced at all. You can either supply your second VCF file or just the CHR and POS columns as tab-separated input to the -R/--regions-file parameter. Please read the manual properly.