Extract a list of mean values from format tags (e.g., DP, GC, IGC, etc.) per position

[andreasgoteson]

Hi,

I have a question (or a feature request): bcftools allows the use of functions on format tags to filter data, but is it possible to just return the result of functions for each position?

For example, I have a multisample vcf with format fields containing per sample information such as Illumina GenCall Confidence Score (IGC)*. I can successfully filter the vcf based on mean IGC (per position), e.g., bcftools view -i 'AVG(FMT/IGC)>0.7' my.vcf. This code correctly returns a filtered vcf retaining only positions where the mean IGC was above 0.7.

But I want to extract a list of all mean values and standard deviations for IGC per position. Is that possible using bcftools?

The output is supposed to look like:
CHROM POS ID mean_IGC sd_IGC
1 1 rs123 0.8 0.05
1 2 rs234 0.5 0.2
...etc

Thanks a lot!

*The IGC is just a score ranging between 0-1 for the genotyping call confidence that is unique for each sample and position.

[pd3]

This is indeed possible. Check the manual please
http://samtools.github.io/bcftools/bcftools.html#query
http://samtools.github.io/bcftools/howtos/query.html

[andreasgoteson]

Sorry, but how? I tried to be very clear when formulating this question, but possibly something is not clear? I have of course carefully read the manual, and checked the provided links again. But I can't see how to extract this data. Would you mind being more specific?

Thanks!

[pd3]

My apologies, I was not reading your question properly.

[pd3]

This is now supported, please try it out.

For example, if the VCF contains INFO/AD and FORMAT/AD, the following should work:

bcftools query test.vcf -f '%CHROM:%POS \t [ %AD]  \t [ %sSUM(FMT/AD)]'
bcftools query test.vcf -f '%CHROM:%POS \t [ %AD]  \t [ %SUM(FMT/AD)]'
bcftools query test.vcf -f '%CHROM:%POS \t [ %AD]  \t   %SUM(FMT/AD)'
bcftools query test.vcf -f '%CHROM:%POS \t [ %AD]  \t   %SUM(INFO/AD)'