## genotype calling
#ANGSD AF
angsd -sites sites.txt -b ceu31.list -doMajorMinor 4 -doMaf 1 -GL 1 -doGeno 19 -doPost 1 -ref  hg19.fa 
#ANGSD ML
angsd -sites sites.txt -b ceu31.list -doMajorMinor 4 -GL 1 -doGeno 19 -doPost 2 -ref hg19.fa
#ANGSD SFS
angsd -sites sites.txt -b ceu31.list -doMajorMinor 4 -GL 1 -doSaf 3 -P 6 -ref  hg19.fa -pest sfs.txt
#SAMtools
./samtools mpileup -f  hg19.fa -b ceu31.list -g -I -l sites.txt |bcftools view -cg  -
#GATK
./gatk -l INFO -R hg19.fa -T HaplotypeCaller -I ceu31.list -L sites.intervals --output_mode EMIT_ALL_SITES 
## computational speed
samtools mpileup -b file.list -f hg19.fa -g -r 21:1-20000000 |bcftools view -v 
gatk -R hg19.fa -T UnifiedGenotyper -I file.list -L 21:1-20000000 -nt 1 
angsd -ref hg19.fa -b file.list -doMaf 1 -GL 1 -P 1 -doMajorMinor 1 -r 21:1-20000000 -snp_pval 1e-5 -checkbamheaders 0