I want to call gvcf with bcftools mpileup containing variant site and reference homologous site blocks The command line shows below
nohup sh -c "bcftools mpileup -C50 -q25 -g 4 -t DP -f reference.fa sample.bam | bcftools call -c | vcfutils.pl varFilter -d4 -D28 > output.g.vcf" &
I also want to filtrate the variant site out which is 2 times of and one third of the average coverage of each sample. However, it only printed the header out and didn't show any variant site or non variant blocks in my output. How should I edit my command line to manipulate vcf files I want?