.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.41.1.
.TH VCF-FIX-PLOIDY "1" "February 2013" "vcf-fix-ploidy" "User Commands"
.SH NAME
vcf-fix-ploidy \- vcf-fix-ploidy
.SH SYNOPSIS
.B cat
\fIbroken.vcf | vcf-fix-ploidy \fR[\fIOPTIONS\fR] \fI> fixed.vcf\fR
.SH OPTIONS
.TP
\fB\-a\fR, \fB\-\-assumed\-sex\fR <sex>
M or F, required if the list is not complete in \fB\-s\fR
.TP
\fB\-l\fR, \fB\-\-fix\-likelihoods\fR
Add or remove het likelihoods (not the default behaviour)
.TP
\fB\-p\fR, \fB\-\-ploidy\fR <file>
Ploidy definition. The default is shown below.
.TP
\fB\-s\fR, \fB\-\-samples\fR <file>
List of sample sexes (sample_name [MF]).
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message.
.SS "Default ploidy definition:"
.IP
ploidy =>
{
.IP
X =>
[
.IP
# The pseudoautosomal regions 60,001\-2,699,520 and 154,931,044\-155,270,560 with the ploidy 2
{ from=>1, to=>60_000, M=>1 },
{ from=>2_699_521, to=>154_931_043, M=>1 },
.IP
],
Y =>
[
.IP
# No chrY in females and one copy in males
{ from=>1, to=>59_373_566, M=>1, F=>0 },
.IP
],
MT =>
[
.IP
# Haploid MT in males and females
{ from=>1, to => 16_569, M=>1, F=>1 },
.IP
],
.IP
}