Number of sites retained after filtering

[shuya099]

hello, teams,

I did haploid calling with the following code:

#!/bin/bash
ref_geno="XXXX"

samtools mpileup -aa -B -l haploid_calling_sites.txt -f "$ref_geno" *.bam > TwoSamps.pileup.txt

After that:

ref_geno_fai="XXXXXX"

angsd -out haploid_calling_output -pileup TwoSamps.pileup.txt -fai "$ref_geno_fai" -nInd 2 -dohaplocall 1 -doCounts 1 -nThreads 5

So the output text shown on the screen was:

    -> Arguments and parameters for all analysis are located in .arg file
    -> Total number of sites analyzed: 42976817
    -> Number of sites retained after filtering: 35524355

I will appreciate it if you can explain what sites got filtered during this process. For pseudohaplotype calling from a known SNP set, there should be no removal of sites at this step, and all samples should end up with the same number of sites.

Many thanks for your help,