I want to call variants from a BAM file with bcftools. To use
call command, I have to use
mpileup command to create a pileup file and use it as input for
call. I run default command like below:
bcftools mpileup -f path_to_reference my_file.bam -o my_file.mpileup
The command above gives me this warning:
[mpileup] maximum number of reads per input file set to -d 250
Then I do variant calling with the command below:
bcftools call -m my_file.mpileup -o my_file.vcf
With these settings, a position's genotype is heterozygous (0/1) and depth is 254.
I override max-depth in mpileup with command below:
bcftools mpileup -d 8000 -f path_to_reference my_file.bam -o my_file.mpileup
Same position's genotype becames homozygous to ref (0/0) and depth is 597.
QUAL values are also different.
Why is this happening and which one I can trust?