I use samtools-bcftools pipeline to call variations among a sample (30 individuals) with low coverage (~5X each).
samtools mpileup -ugf genome.fa -b bam.list -t AD,INFO/AD,DP,SP | bcftools call -vcO z -o out.vcf.gz
In the result, I found some strange heterozygous GTs:
(1) some heterozygous GTs has: DP=0, AD=0, SP=0
(2) many heterozygous GTs have very low DPs:
I don't think it is acceptable to deduce a heterozygous GT if the allele number of REF/ALT is only 3 and 1. The main problem is: How do I avoid such heterozygous GTs ? To add some parameters in samtools mpileup / bcftools call ? or use what software to filter them?