Missing value in ALT alleles for VCF file

[A.R.T]

Hi
I am working on my VCF files (mapped to GRCh37) which contains some missing values in ALT allele site. While there is (.) instead of allele name, the REF allele and variant rs_number in addition to other details are provided. Would you please let me know how can I fix it? Is there any special tool for retrieving missing variants in VCF?

example:

chr22 42523943 rs16947 A .

[dcameron]

It's likely that your coverage at that position is too low for the variant caller to make any call.

> Would you please let me know how can I fix it?

Verify that these variants are indeed called as MISSING due to insufficient coverage. If this is indeed the case, you need to sequence more, or explicitly handle missing variants in your pipeline.

[A.R.T]

It's likely that your coverage at that position is too low for the variant caller to make any call.

> Would you please let me know how can I fix it?

Verify that these variants are indeed called as MISSING due to insufficient coverage. If this is indeed the case, you need to sequence more, or explicitly handle missing variants in your pipeline.

Thank you @dcameron. I noticed that missing positions appeared after I did genome liftover by NCBI tool (https://www.ncbi.nlm.nih.gov/genome/tools/remap). So, my original VCFs do not contain any missing variant. I think I have to choose another tool for converting my GRCh38 vcfs to GRCh37.