Entering edit mode

15 months ago

Timotheus
▴
40

Hello,

I'm filtering my two-sample diploid VCF by, among other filters, coverage (DP) as follows (example for sample with index 1):

```
bcftools filter -i 'FORMAT/DP[1]>90 && FORMAT/DP[1]<140' my.vcf -o my_filtered.vcf
```

I nonetheless discovered that allelic depth (AD) is markedly off at some het sites, i.e., the proportions of the two alleles are far from 50:50. How do I put bounds on these proportions, e.g., so that they are at most 40:60?

Thank you, Pierre: is there no bcftools solution?

But your script works very well, thanks! A pity perhaps it uses a Java expression... how should I apply the filter just to one sample, for example, with index 1?