Hi Sahar,

I get PV4 (P-values for strand bias, baseQ bias, mapQ bias and tail distance bias) and G3 (ML estimate of genotype frequencies) automatically when I align my data with bwa mem and then call variants with samtools mpileup piped into bcftools call (latest versions).

NS (Number of Samples With Data) may be a tag that was used a lot in the past but that has been more or less replaced. You can obtains similar information by looking at the AC (allele count in genotypes, for each ALT allele, in the same order as listed), AF (allele frequency for each ALT allele in the same order as listed: use this when estimated from primary data, not called genotypes), and AN (total number of alleles in called genotypes) tags.

The same may be true for BQ (RMS base quality at this position). However, using samtools mpileup, you can ensure a minimal base quality on variant bases with the --min-BQ comman-lime parameter.