I have a low coverage (1.0x) fastq sample.
I am following GATK best practices pipeline (bwa mem > Mark Duplicates > BQSR > Apply BQSR > HaplotypeCaller) to produce the VCF from fastq.
When comparing the resulted VCF with the ground truth, it performs well on homozygous variants but terribly on heterozygous (responsible for 99% mismatches).
(I also tried DeepVariant. I obtain similar results.)
How should I modify the pipeline for a low coverage sample? (Is there extra work required on .bam file or some special configuration of Haplotypecaller,...?)