angsd -bam
...
parseArgs_bambi.cpp: bam reader:
    -bam/-b        (null)    (list of BAM/CRAM files)
    -i        (null)    (Single BAM/CRAM file)
    -r        (null)    Supply a single region in commandline (see examples below)
    -rf        (null)    Supply multiple regions in a file (see examples below)
    -remove_bads    1    Discard ‘bad‘ reads, (flag >=256) 
    -uniqueOnly    0    Discards reads that doesn‘t map uniquely
    -show        0    Mimic ‘samtools mpileup‘ also supply -ref fasta for printing reference column
    -minMapQ    0    Discard reads with mapping quality below
    -minQ        13    Discard bases with base quality below
    -trim        0    Number of based to discard at both ends of the reads
    -trim        0    Number of based to discard at 5‘ ends of the reads
    -trim        0    Number of based to discard at 3‘ ends of the reads
    -only_proper_pairs 1    Only use reads where the mate could be mapped
    -C        0    adjust mapQ for excessive mismatches (as SAMtools), supply -ref
    -baq        0    adjust qscores around indels (1=normal baq 2= extended(as SAMtools)), supply -ref
    -redo-baq        0 (recompute baq, instead of using BQ tag)
    -checkBamHeaders 1    Exit if difference in BAM headers
    -doCheck    1    Keep going even if datafile is not suffixed with .bam/.cram
    -downSample    0.000000    Downsample to the fraction of original data
    -nReads        50    Number of reads to pop from each BAM/CRAMs
    -minChunkSize    250    Minimum size of chunk sent to analyses
    --ignore-RG    1    (dev only)
    +RG    (null)    Readgroups to include in analysis(can be filename)

Examples for region specification:
        chr:        Use entire chromosome: chr
        chr:start-    Use region from start to end of chr
        chr:-stop    Use region from beginning of chromosome: chr to stop
        chr:start-stop    Use region from start to stop from chromosome: chr
        chr:site    Use single site on chromosome: chr

multiReader.cpp:
        -nLines 50      (Number of lines to read)
        -beagle (null)  (Beagle Filename (can be .gz))
        -vcf-GL (null)  (vcf Filename (can be bcf compressed or uncompressed))
        -vcf-PL (null)  (vcf Filename (can be bcf compressed or uncompressed))
        -vcf-GP (null)  (vcf Filename (can be bcf compressed or uncompressed))(*not used)
        -glf    (null)  (glf Filename (can be .gz))
        -pileup (null)  (pileup Filename (can be .gz))
        -intName 1      (Assume First column is chr_position)
        -isSim  0       (Simulated data assumes ancestral is A)
        -nInd   0               (Number of individuals)
        -minQ   13      (minimum base quality; only used in pileupreader)
        -fai    (null)  (fai file)
        -minQ   13      (minimum base quality; only used in pileupreader)

angsd -GL
...
-GL=0: 
    1: SAMtools
    2: GATK
    3: SOAPsnp
    4: SYK
    5: phys
    6: Super simple sample an allele type GL. (1.0,0.5,0.0)
    7: outgroup gls
    -trim        0        (zero means no trimming)
    -tmpdir        angsd_tmpdir/    (used by SOAPsnp)
    -errors        (null)        (used by SYK)
    -minInd        0        (0 indicates no filtering)

Filedumping:
    -doGlf    0
    1: binary glf (10 log likes)    .glf.gz
    2: beagle likelihood file    .beagle.gz
    3: binary 3 times likelihood    .glf.gz
    4: text version (10 log likes)    .glf.gz

angsd -doMajorMinor
...
        -doMajorMinor   0
        1: Infer major and minor from GL
        2: Infer major and minor from allele counts
        3: use major and minor from a file (requires -sites file.txt)
        4: Use reference allele as major (requires -ref)
        5: Use ancestral allele as major (requires -anc)
        -rmTrans: remove transitions 0
        -skipTriallelic 0

angsd -doMaf
...
-doMaf  0 (Calculate persite frequencies ‘.mafs.gz‘)
        1: Frequency (fixed major and minor)
        2: Frequency (fixed major unknown minor)
        4: Frequency from genotype probabilities
        8: AlleleCounts based method (known major minor)
        NB. Filedumping is supressed if value is negative
-doPost 0       (Calculate posterior prob 3xgprob)
        1: Using frequency as prior
        2: Using uniform prior
        3: Using SFS as prior (still in development)
        4: Using reference panel as prior (still in development), requires a site file with chr pos major minor af ac an
Filters:
        -minMaf         -1.000000       (Remove sites with MAF below)
        -SNP_pval       1.000000        (Remove sites with a pvalue larger)
        -rmTriallelic   0.000000        (Remove sites with a pvalue lower)
Extras:
        -ref    (null)  (Filename for fasta reference)
        -anc    (null)  (Filename for fasta ancestral)
        -eps    0.001000 [Only used for -doMaf &8]
        -beagleProb     0 (Dump beagle style postprobs)
        -indFname       (null) (file containing individual inbreedcoeficients)
        -underFlowProtect       0 (file containing individual inbreedcoeficients)
NB These frequency estimators requires major/minor -doMajorMinor