Vcf Filtering

Question

[Marc Ibanez]

Hi, I recently obtained a vcf file with 90 samples from different generations. I realized that the file is extremely large. This is because I have a lot of possible sequencing errors, observing AF really closed to 0 or 1, and only in one of the samples out of 90. For this reason, I want to filter the whole file, selecting only the SNPs which at least in one sample has a value between 0.15 and 0.85. Do you know how can I do it?

I tried with this code "bcftools view -i 'sum(AF >= 0.15 && AF <= 0.85) > 0'" but it didn't gave me the expected result. Thank you!

[Pierre Lindenbaum]

AF is usually an INFO field, not a FORMAT/genotype field. What is the definition of AF in your header file and please, give us an example of such genotypes.

[Marc Ibanez]

Hi, the definition of AF in my header is this one:

##FORMAT=<ID=AF,Number=A,Type=Float,Description="Observed ALT frequencies"> . And here I add an example of the genotype: GT:PL:DP:AD:SCR:QS:SAD:AF:XF    ./.:.:48:19,21:12:540,524:40:0.525:0.511628     ./.:.:42:24,13:9:537,305:37:0.351351:0.35. 

Thank you in advance

[Jeremy Leipzig]

I don't understand what AF refers to in this scenario when the genotype is ./.

Are these diploid organisms?

Answer 1

[Pierre Lindenbaum]

using vcffilterjdk https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/

java -jar dist/jvarkit.jar vcffilterjdk -e 'return variant.getGenotypes().stream().anyMatch(G->{double v=G.getAttributeAsDouble("AF",-1);return v>=0.15 && v<=0.85;});'  in.vcf