keep samples that carry non-reference allele in list of variants snpeff/snpsift

Question

[curious]

I am trying to get carriers of high impact variants of DUOX2 with the amazing snpeff/snpsift workflow

I annotate:

snpEff -Xmx64g "hg38" $sample.vcf.gz > $sample_annotated.vcf

I filter keeping variants with high impact in DUOX2

bcftools view  $sample_annotated.vcf  | SnpSift filter "( EFF[*].IMPACT = 'HIGH' ) & ( EFF[*].GENE = 'DUOX2' )" > $variant_filt.vcf

Now I want to keep only samples that have at least one non-homozygous reference genotype in any of the high impact variants. Is there a way to do this with snpeff or some other tool?

Answer 1

[Pierre Lindenbaum]

after filtering the variant with snpEff, get the samples carrying an ALT using http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

java -jar ${JVARKIT_DIST}/bioalcidaejdk.jar -e 'stream().flatMap(V->V.getGenotypes().stream()).filter(G->G.isCalled() && G.getAlleles().stream().anyMatch(A->A.isNonReference())).map(G->G.getSampleName()).collect(Collectors.toSet()).stream().forEach(S->println(S));' filtered.snpsift.vcf > samples.txt

use samples with bcftools to extract those samples:

bcftools view --samples-file samples.txt -O u filtered.snpsift.vcf | bcftools view -i 'AC>0'

[curious]

That certainty looks like it is working, but I get error:

[WARN][SnpEffPredictionParser]no INFO[EFF] or no description. This VCF was probably NOT annotated with SnpEff (old version)

I know I could rerun snpEff with -formatEff, but your command is not using these annotations right? If I understand the assumption is that I am filtering on the snpeff annotations prior to your command and that your command is just passing genotypes correct?

[Pierre Lindenbaum]

this is just a warning. you can ignore this as your vcf is already filtered.

[curious]

Thank you so much