I first do samtools mpileup:
samtools mpileup -uf /mnt/NAS/share/Ref/human/hs37d5.fa -l 1000G.bed -q 30 -Q 30 in.bam -o out.bcf
Then: I can call snps from the bcf with at least two different commands:
bcftools call -mV indels bcftools call -c -v
I get two vastly different results with these.
I don't know which one is correct and how I should actually do this.