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Old 06-27-2016, 08:37 AM   #1
lstbl
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Location: USA

Join Date: Aug 2015
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Default confusion about BCFtools "EXPRESSIONS" flags

I'm hoping someone can help me understand the "EXPRESSIONS" flags used in bfctools.

I'm trying to filter variants from a vcf file produced using the 'mpileup' program from samtools. Essentially, I want to perform a simple filtering step that will exclude all reads that don't pass a threshold (say, > 30% of the reads sequenced at that position)

This is what I I'm using now:
bcftools filter -i'%MIN(DV/DP)>.3' --output-type v -o mpileup.vcf

However, I'm a bit confused about the proper usage of "MIN".

According the bfctools documentation page, "MIN" should be used with "on FORMAT tags (over samples) and INFO tags (over vector fields)" see https://samtools.github.io/bcftools/...ml#expressions

However, I have no clue what this means. I'm not sure if I should drop the MIN and just filter using -i'%(DV/DP)>0.3'.
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