Hello,

I used bwa for alignment and I am using gvcf for calling variants with this code:

bcftools mpileup -Ov --gvcf 5 -f ref.fa example.sorted.bam | bcftools call -m --gvcf 5 -o example.vcf

I want to keep the homozygous reference calls to distinguish them from any missing calls. I am only interested in SNP variants so after getting the gvcf, I used:

bcftools view --exclude-types indels,mnps,bnd,other example.vcf -o example_1.vcf

I want to use this file for some downstream analysis by merging it with other similar gvcf files. But I noticed that in example.vcf, there are some positions not called at all which have minimum read depth of 5 as I specified in mpileup and call steps. I am pasting some lines from example.vcf:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT sample.sorted.bam
ch01    195 .   G   .   29.5864 .   DP=1;MQ0F=0;AN=0;DP4=0,0,0,0;MQ=.   GT:DP   ./.:0
ch01    196 .   T   .   29.5864 .   DP=1;MQ0F=0;AN=0;DP4=0,0,0,0;MQ=.   GT:DP   ./.:0
ch01    198 .   A   .   29.5864 .   DP=1;MQ0F=0;AN=0;DP4=0,0,0,0;MQ=.   GT:DP   ./.:0

In IGV, position 197 has enough reads but gvcf file does not include it. I am not sure why? Thank you for your help!