Excluding variants with a "LowQual" filter in bcftools consensus

Question

[cg1440]

Greetings.

I'm running the basic pipeline to call variants and generate consensus sequences using bcftools: mpileup | call | filter low qual variants (set FILTER to "LowQual") | consensus.

However, bcftools consensus is still counting low quality variants and outputting them as variants in the consensus genome. Is there a way to exclude such low quality variants?

Thanks.

Answer 1

[finswimmer]

bcftools consensus have an --include and --exclude paramater, which you can use to inlcude/exclude variants that should be used for the consensus. (See docs)

So a bcftools consensus --exclude FILTER="LowQual" should work.

[Pierre Lindenbaum]

--exclude 'FILTER~"LowQual"'

http://samtools.github.io/bcftools/bcftools.html

starting with 1.11, the FILTER column can be queried as follows:

FILTER="A" .. exact match, for example "A;B" does not pass

FILTER!="A" .. exact match, for example "A;B" does pass

[cg1440]

It seems that it's working. Thanks!

[cg1440]

Thank you for your input. You guided me to the right path, although your syntax did not work. I used 'FILTER~"LowQual"' as highlighted by the other reply.