<p>Is there a good way to distinguish ./. from 0/0 in a merged vcf? For example, a tool that goes back to the bam files for missing genotypes and checks if it&#39;s homozygous reference or a NO CALL? I would imagine this would be important to do, especially in 30x WGS where there are a lot of low coverage areas that lead to no calls.</p>

<p>Although, I guess if you have the bam files maybe the best thing to do is joint variant calling?</p>

I just wrote http://lindenb.github.io/jvarkit/FixVcfMissingGenotypes.html It takes a merged VCF and uses the original Bams to fill the missing genotypes. . If the number of reads is greater than **min.depth**, then the missing genotype is said hom-ref. This tool is very new/alpha, use the github issue tracker to tell me if there is a problem please.

**Usage:**

```
$ yourtool-mergingvcf 1.vcf 2.vcf 3.vcf > merged.vcf
$ find ./ -name "*.bam" > bams.txt
$  java -jar dist/fixvcfmissinggenotypes.jar -f bams.txt merged.vcf > out.vcf
```