Filter vcf SNPs by sample GT value

Question

[hlebnikovdaniil]

I have a merged VCF file with multiple samples on joined SNP set, where original genotypes have a 0|0 / 0|1 / 1|0 / 1|1 genotype (GT) and merged are fomatted as 0/0 if SNP was missing (--missing-ref option of bcftools merge). I'd like to filter the file to only have those SNPs that don't have 0/0 in GT field of last two columns. Here's an excerpt from a vcf file (header and first two example lines):

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  orig_s1 orig_s2 orig_s3  merged_s1 merged_s2
chr5    11875   .       G       A       .       PASS    VT=SNP;NS=2548;DP=1908;AF=0.05;EAS_AF=0;EUR_AF=0.01;AFR_AF=0.17;AMR_AF=0.02;SAS_AF=0.02;AN=5100;AC=267  GT      1|0     0|0     0|0     0/0     0/0
chr5    11956   .       G       C       .       PASS    VT=SNP;NS=2548;DP=13160;AF=0.03;EAS_AF=0;EUR_AF=0;AFR_AF=0.11;AMR_AF=0.01;SAS_AF=0;AN=5100;AC=148       GT      0|0     0|0     0|0     1|1     0/0
chr5    11989   .       G       A       .       PASS    VT=SNP;NS=2548;DP=14138;AF=0;EAS_AF=0;EUR_AF=0;AFR_AF=0;AMR_AF=0;SAS_AF=0;AN=5100;AC=1                  GT      0|0     0|0     0|0     0/0     1|1
chr5    12002   .       G       C       .       PASS    VT=SNP;NS=2548;DP=14197;AF=0;EAS_AF=0;EUR_AF=0;AFR_AF=0;AMR_AF=0;SAS_AF=0;AN=5100;AC=2                  GT      0|0     0|0     0|0     1|1     1|1

So for this example here I'd like to filter out first entry but not the ones after. I have tried: bcftools view -i 'FORMAT/GT[4] != "0/0" | FORMAT/GT[5] != "0/0"', but this doesn't seem to work. Any help would be appreciated to solve this issue. Thanks!

Answer 1

[Pierre Lindenbaum]

with GATK selectVariant https://gatk.broadinstitute.org/hc/en-us/articles/360037055952-SelectVariants a JEXL select expression (not tested)

'!vc.getGenotype(4).isHomRef() && !vc.getGenotype(5).isHomRef()'

Answer 2

[Axzd]

You are using a pipe wich means "or", but from your wording, you want to exclude SNP with a GT of 0/0 in both the last 2 samples. So, if this is the case, replace "|" with "&" in your command and see if it gives you what you want.