parser.add_argument('-H',help='specify if HEADER of vcf file should be ommitted [default: False]',action='store_true')
parser.add_argument('-chr',help='secify chromosomes to be parsed as a comma-seperated list')
parser.add_argument('-filterarg',help='specify FILTER arguments to keep variants, all variants without these will be discarded. ' \
'use a comma-seperated list e.g. PASS,VQSRTTranchesSNP90. ' \
'By default all variants are retained [default: ""]',default='')
parser.add_argument('-samples',help='specify sample names to be merged as a comma-seperated list, they need to exactly match sample ids from vcf input')
parser.add_argument('-add',help='specify if CONSENSUS should be added as a new column to existing vcf file [default: False]',action='store_true')
parser.add_argument('-id',help='specify CONSENSUS name to be added to HEADER')
parser.add_argument('-minMQ',help='specify mapping quality threshold necessary to exceeded to retain variant [default: "0.0"]',type=float,default=0.0)
parser.add_argument('-missingGT',help='specify how missing GT data (based on e.g. calling SNPs with GATK on multiple samples simultaneously; GT: ./.) ' \
'should be handled, either keep AD coverage [default: "keep"], set AD to 0 for all samples which have GT: ./. for all alleles ["zero"], ' \
'set REF allele to certain value and ALT alleles to certain value for all samples that have GT: ./. ["set:value:value"] e.g. ref:10:10 ' \
'NOTE: there might be cases where the VariantCaller has defined GT: ./. however AD still shows counts AD: 3,0 ' \
'here one might not want to keep this variant as NotCalled (GT: ./.) and use the AD information to reset GT based on AD',default='keep')
parser.add_argument('-resetGT',help='specify how GT should be reset, either reset using AD information [default: "AD"] or keep as defined by VariantCaller ["keep"] ' \
'NOTE: the DP value needs to be exceeded otherwise the sample will be set to ./. ' \
'NOTE: this will influence the calculation of the NotCalledFraction',default='AD',choices=['AD','keep'])
parser.add_argument('-minDP',help='specify minimal sample depth threshold to set position to be NotCalled during GT reset [default: "0"]',type=int,default=0)
parser.add_argument('-maxDP',help='specify maximal sample depth threshold to set position to be NotCalled during GT reset [default: "9999999"]',type=int,default=9999999)
parser.add_argument('-minGQ',help='specify minimal genotype quality threshold to set position to Called during GT reset [default: "0"]',type=int,default=0)
parser.add_argument('-ncf',help='specify NotCalledFraction to exclude SNP/MNP [default: "1.0"] for consensus calculation',type=float,default=1.0)
parser.add_argument('-cdp',help='specify consensus depth threshold necessary to exceeded to retain SNP/MNP [default: "5"]' \
'NOTE: only Called samples will be considered after GT reset',type=int,default=5)
parser.add_argument('-po',help='specify if progress should not be printed based on variant number processed [default: False]',action='store_true')