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gnomit.38.cram.pl
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gnomit.38.cram.pl
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#!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
my $version = "0.0.23";
# version update
# 0.0.23
# -added option to require a minimum level of evidence for sample level genotyping
#
# 0.0.22
# -updated version to be consistent with dinumt package
#
# 0.0.16
# -fixed program with too many supporting reads crashing GL calculation
# -updated output to include more original INFO tag information
#
# 0.0.15
# -added option to turn off EM iterations
#
# 0.0.14
# -added MT mapping check for clipped sequences at potential breakpoints
#
# 0.0.13
# -fixed error with likelihood calculation
# -added support for by_chr_dir genotyping
#
# 0.0.12
# -added per-read mapQ errors with likelihood calculation
#
# 0.0.11
# -updated supporting read determination
#
# 0.0.10
# -integrated RP and SR liklihoods, when available
#
# 0.0.9
# -incorporated EM algorithm for implementing allele frequency priors
#
# 0.0.8
# -updated support counting around breakpoints
#
# 0.0.7
# -modified scoring to implement bayesian scoring of evidence
# -incorporated insert length cutoff for alternative allele determination
#
# 0.0.6
# -fixed bug where altSR was not being initialized correctly
# -removed max_read_cov filter in report()
#
# 0.0.5
# -added --chr option for by-chromosome analysis
#
# 0.0.4
# -bug fixes
#
# 0.0.3
# -modified scoring function to better assess clipping in breakpoint determination and scoring
# -modified rp scoring to not consider reads clipped at breakpoint as reference
#
# 0.0.2
# -modified input parameters to expect VCF format
#
# 0.0.1
# -initial version
my %opts = ();
$opts{len_cluster_include} = 600;
$opts{len_cluster_link} = 800;
$opts{min_reads_cluster} = 1;
$opts{min_clipped_seq} = 5;
$opts{clipped_flank} = 50;
$opts{max_num_clipped} = 5;
$opts{include_mask} = 0;
$opts{min_evidence} = 3;
$opts{min_map_qual} = 10;
$opts{filter_qual} = 13;
$opts{filter_depth} = 5;
$opts{max_read_cov} = 200;
$opts{use_priors} = 0;
$opts{mask_filename} = "/home2/remills/projects/numts/numtS.bed";
$opts{info_filename} = "/scratch/remills_flux/remills/sampleInfo.txt";
$opts{reference} = "/nfs/remills-scratch/reference/hs37d5/hs37d5.fa";
$opts{mt_filename} = "/nfs/remills-scratch/reference/GRCh37/Sequence/Chromosomes/MT.fa";
$opts{samtools} = "/home2/remills/bin/samtools";
$opts{exonerate} = "/home2/remills/apps/exonerate-2.2.0/bin/exonerate";
$opts{dir_tmp} = "/tmp";
$opts{prefix} = "numt";
$opts{len_mt} = 16596; #eventually should be read in by BAM header
$opts{ploidy} = 2;
my $optResult = GetOptions(
"input_filename=s" => \$opts{input_filename},
"output_filename=s" => \$opts{output_filename},
"mask_filename=s" => \$opts{mask_filename},
"info_filename=s" => \$opts{info_filename},
"mt_filename=s" => \$opts{mt_filename},
"dir_tmp=s" => \$opts{dir_tmp},
"chr=s" => \$opts{chr},
"include_mask" => \$opts{include_mask},
"len_cluster_include=i" => \$opts{len_cluster_include},
"len_cluster_link=i" => \$opts{len_cluster_link},
"min_reads_cluster=i" => \$opts{min_reads_cluster},
"min_evidence=i" => \$opts{min_evidence},
"min_clipped_seq=i" => \$opts{min_clipped_seq},
"max_num_clipped=i" => \$opts{max_num_clipped},
"min_map_qual=i" => \$opts{min_map_qual},
"max_read_cov=i" => \$opts{max_read_cov},
"read_groups" => \$opts{read_groups},
"breakpoint" => \$opts{breakpoint},
"reference=s" => \$opts{reference},
"samtools=s" => \$opts{samtools},
"exonerate=s" => \$opts{exonerate},
"use_priors" => \$opts{use_priors},
"by_chr_dir" => \$opts{by_chr_dir},
"prefix=s" => \$opts{prefix},
"ucsc" => \$opts{ucsc},
"help" => \$opts{help},
"verbose" => \$opts{verbose}
);
checkOptions( $optResult, \%opts, $version );
my $seq_num = 0;
my %seq_hash = ();
my %sorted_hash = ();
my $i = 1;
my %sample_hash = ();
my %infile_hash = ();
my %group_hash = ();
my %outfile_hash = ();
my %mask_hash = ();
my %data_hash = ();
getInput( \%infile_hash, \%mask_hash, \%sample_hash );
getData( \%infile_hash, \%mask_hash, \%sample_hash, \%data_hash );
if ($opts{breakpoint}) {
assessBreaks( \%infile_hash, \%sample_hash, \%data_hash );
}
refineData( \%infile_hash, \%mask_hash, \%sample_hash, \%data_hash );
scoreData( \%data_hash, \%sample_hash );
report( \%infile_hash, \%data_hash );
################################################################################################################
sub mappedClippedSeq {
my ($clipSeq) = @_;
if ( $clipSeq =~ /N/ ) { return 0; }
my $random = int( rand(100000) );
my @timeData = localtime(time);
my $timestamp = join( '', @timeData );
my $fileClp = "$opts{dir_tmp}/clp$timestamp$random.fa";
open( CLP, ">$fileClp" );
print CLP ">clp\n$clipSeq\n";
close CLP;
my $results = `$opts{exonerate} --model affine:local --exhaustive yes --percent 70 --showvulgar no --showalignment no --showcigar yes $fileClp $opts{mt_filename} 2> /dev/null`;
my ( $query_id, $query_start, $query_end, $query_strand, $target_id, $target_start, $target_end, $target_strand, $score, $cigar ) = $results =~ /cigar\:\s+(\S+)\s+(\d+)\s+(\d+)\s+(\+|-)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\+|-)\s+(\d+)\s+(.*?)\n/;
`rm $fileClp`;
if ($cigar) { return 1; }
else { return 0; }
}
sub assessBreaks {
my ( $infile_hash, $sample_hash, $data_hash ) = @_;
print "Entering assessBreaks()\n" if $opts{verbose};
foreach my $var ( keys %$data_hash ) {
print "-variant $var\n" if $opts{verbose};
my %clippedPos = ();
my %clippedSeq = ();
my $sumClipped = 0;
my $winStart = 1e10;
my $winEnd = 0;
my $maxFirst = 0;
my $maxSecond = 0;
foreach my $sample ( keys %{ $data_hash{$var} } ) {
foreach my $cPos ( keys %{ $data_hash{$var}{$sample}{clipPos} } ) {
next if $cPos == -1;
if ( defined( $data_hash{$var}{$sample}{clipPos}{$cPos}{1} ) ) {
if ( mappedClippedSeq( $data_hash{$var}{$sample}{clipSeq}{$cPos} ) ) {
$clippedPos{$cPos} += $data_hash{$var}{$sample}{clipPos}{$cPos}{1};
$sumClipped += $data_hash{$var}{$sample}{clipPos}{$cPos}{1};
#if (!defined($clippedSeq{$cPos} || length($data_hash{$var}{$sample}{clipSeq}{$cPos}) > $clippedSeq{$cPos})) { $clippedSeq{$cPos} = $data_hash{$var}{$sample}{clipSeq}{$cPos}; }
}
}
}
}
my $winLen = scalar keys %clippedPos;
my @sorted = sort { $clippedPos{$b} <=> $clippedPos{$a} } keys %clippedPos;
if ( $winLen == 0 ) { next; }
elsif ( $winLen == 1 ) {
$infile_hash{$var}{leftBkpt} = $sorted[0];
$infile_hash{$var}{rightBkpt} = $sorted[0] + 1;
}
elsif ( $winLen == 2 ) {
$infile_hash{$var}{leftBkpt} = $sorted[0];
$infile_hash{$var}{rightBkpt} = $sorted[0] + 1;
if ( $sorted[1] > $sorted[0] ) {
$infile_hash{$var}{rightBkpt} = $sorted[1];
}
else {
$infile_hash{$var}{leftBkpt} = $sorted[1];
$infile_hash{$var}{rightBkpt}--;
}
}
else {
my @sorted = sort { $clippedPos{$b} <=> $clippedPos{$a} } keys %clippedPos;
my $meanClipped = $sumClipped / $winLen;
my $sumSquares = 0;
print "\tmean clipped: $meanClipped\n" if $opts{verbose};
#for ( my $p = $winStart ; $p <= $winEnd ; $p++ ) {
# if ( !defined( $clippedPos{$p} ) ) { $clippedPos{$p} = 0; }
# $sumSquares += ( $clippedPos{$p} - $meanClipped )**2;
#}
foreach my $cPos ( keys %clippedPos ) {
$sumSquares += ( $clippedPos{$cPos} - $meanClipped )**2;
}
my $sdClipped = sqrt( $sumSquares / ( $winLen - 1 ) );
print "\tsd clipped: $sdClipped\n" if $opts{verbose};
print "\t1st clipped: $clippedPos{ $sorted[0] }\n" if defined( $sorted[0] ) && $opts{verbose};
print "\t2nd clipped: $clippedPos{ $sorted[1] }\n" if defined( $sorted[1] ) && $opts{verbose};
if ( defined( $sorted[0] ) && $clippedPos{ $sorted[0] } > $meanClipped + 1 * $sdClipped ) {
print "\t*updating to 1st\n" if $opts{verbose};
$infile_hash{$var}{leftBkpt} = $sorted[0];
$infile_hash{$var}{rightBkpt} = $sorted[0] + 1;
}
if ( defined( $sorted[1] ) && $clippedPos{ $sorted[1] } > $meanClipped + 1 * $sdClipped ) {
print "\t*updating to 1st and 2nd\n" if $opts{verbose};
if ( $sorted[1] > $sorted[0] ) {
$infile_hash{$var}{rightBkpt} = $sorted[1];
}
else {
$infile_hash{$var}{leftBkpt} = $sorted[1];
$infile_hash{$var}{rightBkpt}--;
}
}
}
print "-variant $var completed\n" if $opts{verbose};
}
print "Exiting assessBreaks()\n\n" if $opts{verbose};
}
sub scoreData {
my ( $data_hash, $sample_hash ) = @_;
print "Entering scoreData()\n" if $opts{verbose};
foreach my $var ( keys %$data_hash ) {
print "Variant: $var\n" if $opts{verbose};
my %priors = ();
my %genoFreq = ();
foreach my $geno ( 0 .. $opts{ploidy} ) {
#start with uniform priors
$priors{$geno} = 1 / ( $opts{ploidy} + 1 );
$genoFreq{$geno}{old} = 0;
$genoFreq{$geno}{new} = 0;
}
my $numIteration = 0;
my $sumGenoFreq = 0;
while ( $numIteration < 10 ) {
$numIteration++;
foreach my $sample ( keys %{$sample_hash} ) {
print "\tSample: $sample\n" if $opts{verbose};
#zero out alternative supporting evidence if below threshold
if ($$data_hash{$var}{$sample}{numAltRP} + $$data_hash{$var}{$sample}{numAltSR} < $opts{min_evidence}) {
$$data_hash{$var}{$sample}{numAltRP} = 0;
$$data_hash{$var}{$sample}{numAltSR} = 0;
$$data_hash{$var}{$sample}{qualAltRP} = ();
$$data_hash{$var}{$sample}{qualAltSR} = ();
}
my $numRefRP = $$data_hash{$var}{$sample}{numRefRP};
my $numAltRP = $$data_hash{$var}{$sample}{numAltRP};
my $numRefSR = $$data_hash{$var}{$sample}{numRefSR};
my $numAltSR = $$data_hash{$var}{$sample}{numAltSR};
foreach my $geno ( 0 .. $opts{ploidy} ) {
$$data_hash{$var}{$sample}{pl}{$geno} = 0;
$$data_hash{$var}{$sample}{gl}{$geno} = 0;
$$data_hash{$var}{$sample}{gl0}{$geno} = 0;
}
$$data_hash{$var}{$sample}{gq} = 0;
$$data_hash{$var}{$sample}{gt} = "./.";
$$data_hash{$var}{$sample}{ft} = "LowQual";
if ( $numAltRP + $numRefRP + $numAltSR + $numRefSR == 0 ) { next; }
if ( $$data_hash{$var}{$sample}{avgQ} <= 0 || $$data_hash{$var}{$sample}{avgQ} > 1 ) { $$data_hash{$var}{$sample}{avgQ} = 0.999999; }
$$data_hash{$var}{$sample}{avgQ} = 0.00001;
foreach my $g ( 0 .. $opts{ploidy} ) {
my $geno = $opts{ploidy} - $g; #need to reverse as calculation is reference allele based
if ( $numAltRP + $numRefRP > 0 && 1 / $opts{ploidy} ** ($numAltRP + $numRefRP) > 0) {
$$data_hash{$var}{$sample}{gl0}{$geno} += calcGl( $opts{ploidy}, $g, $numAltRP + $numRefRP, $numRefRP, $$data_hash{$var}{$sample}{qualRefRP}, $$data_hash{$var}{$sample}{qualAltRP} );
}
if ( $numAltSR + $numRefSR > 0 && $opts{breakpoint} && 1 / $opts{ploidy} ** ($numAltSR + $numRefSR) > 0) {
$$data_hash{$var}{$sample}{gl0}{$geno} += calcGl( $opts{ploidy}, $g, $numAltSR + $numRefSR, $numRefSR, $$data_hash{$var}{$sample}{qualRefSR}, $$data_hash{$var}{$sample}{qualAltSR} );
}
print "\tgl0 returned from calcGL() for geno $geno: $$data_hash{$var}{$sample}{gl0}{$geno}\n" if $opts{verbose};
if ( $$data_hash{$var}{$sample}{gl0}{$geno} < -255 ) { $$data_hash{$var}{$sample}{gl0}{$geno} = -255; } #capped
$$data_hash{$var}{$sample}{gl}{$geno} = log10( $priors{$geno} ) + $$data_hash{$var}{$sample}{gl0}{$geno}; #adjust with population inferred prior
}
my @sortedGeno = sort { $$data_hash{$var}{$sample}{gl}{$b} <=> $$data_hash{$var}{$sample}{gl}{$a} } keys %{ $$data_hash{$var}{$sample}{gl} };
#calculate PL from GL
foreach my $geno ( 0 .. $opts{ploidy} ) {
print "\tcalculating pl from geno ($$data_hash{$var}{$sample}{gl}{$geno})\n" if $opts{verbose};
$$data_hash{$var}{$sample}{pl}{$geno} = int( -10 * $$data_hash{$var}{$sample}{gl}{$geno} );
if ( $$data_hash{$var}{$sample}{pl}{$geno} > 255 ) { $$data_hash{$var}{$sample}{pl}{$geno} = 255; }
print "\t...$$data_hash{$var}{$sample}{pl}{$geno}\n" if $opts{verbose};
}
#normalize PL to most likely genotype
foreach my $geno ( 0 .. $opts{ploidy} ) {
$$data_hash{$var}{$sample}{pl}{$geno} -= $$data_hash{$var}{$sample}{pl}{ $sortedGeno[0] };
}
#determine genotype quality
$$data_hash{$var}{$sample}{gq} = int( 10 * ( $$data_hash{$var}{$sample}{gl}{ $sortedGeno[0] } - $$data_hash{$var}{$sample}{gl}{ $sortedGeno[1] } ) );
print "\t...$$data_hash{$var}{$sample}{gq}\n" if $opts{verbose};
my $gt = "0/0";
if ( $sortedGeno[0] == 1 ) { $gt = "0/1"; }
elsif ( $sortedGeno[0] == 2 ) { $gt = "1/1"; }
$$data_hash{$var}{$sample}{gt} = $gt;
if ( $numAltRP + $numRefRP + $numAltSR + $numRefSR < $opts{filter_depth} || $$data_hash{$var}{$sample}{gq} < $opts{filter_qual} ) { $$data_hash{$var}{$sample}{ft} = "LowQual"; }
else { $$data_hash{$var}{$sample}{ft} = "PASS"; }
$genoFreq{ $sortedGeno[0] }{new}++;
$sumGenoFreq++;
}
my $isConverged = 1;
if ( $sumGenoFreq == 0 ) { warn "no genotypes passing filters\n"; last; }
foreach my $geno ( 0 .. $opts{ploidy} ) {
if ( $genoFreq{$geno}{new} == 0 ) {
$priors{$geno} = 1 / $sumGenoFreq;
}
else {
$priors{$geno} = $genoFreq{$geno}{new} / $sumGenoFreq;
}
if ( $genoFreq{$geno}{old} != $genoFreq{$geno}{new} ) { $isConverged = 0; }
$genoFreq{$geno}{old} = $genoFreq{$geno}{new};
$genoFreq{$geno}{new} = 0;
}
if ($isConverged || !$opts{use_priors}) { last; }
}
}
print "Exiting scoreData()\n\n" if $opts{verbose};
}
sub getDate {
my ( $second, $minute, $hour, $dayOfMonth, $month, $yearOffset, $dayOfWeek, $dayOfYear, $daylightSavings ) = localtime();
my $year = 1900 + $yearOffset;
$month++;
my $fmonth = sprintf( "%.2d", $month );
my $fday = sprintf( "%.2d", $dayOfMonth );
return "$year$fmonth$fday";
}
sub report {
my ( $infile_hash, $data_hash ) = @_;
print "Entering report()\n" if $opts{verbose};
#open output file
if ( defined( $opts{output_filename} ) ) {
open( foutname1, ">$opts{output_filename}" ) or die("error opening file $opts{output_filename}\n");
}
else {
open( foutname1, ">&", \*STDOUT ) or die;
}
my $filedate = getDate();
print foutname1 <<HEADER;
##fileformat=VCFv4.1
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=INS:MT,Description="Nuclear Mitochondrial Insertion">
##FILTER=<ID=LowQual,Description="No PASS calls in any sample after merging">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number likelihoods">
##FORMAT=<ID=CNL0,Number=.,Type=Float,Description="Copy number likelihoods with no frequency prior">
##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">
##FORMAT=<ID=GL0,Number=G,Type=Float,Description="Genotype likelihoods with no frequency prior">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of this variant">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=MSTART,Number=1,Type=Flag,Description="Mitochondrial start coordinate of inserted sequence">
##INFO=<ID=MEND,Number=1,Type=Flag,Description="Mitochondrial end coordinate of inserted sequence">
##INFO=<ID=MLEN,Number=1,Type=Flag,Description="Estimated length of mitochondrial insert">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation">
##INFO=<ID=SAMPLES,Number=.,Type=String,Description="Sample(s) in which site was originally discovered">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chrY,length=57227415>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr15_KI270905v1_alt,length=5161414>
##contig=<ID=chr6_GL000256v2_alt,length=4929269>
##contig=<ID=chr6_GL000254v2_alt,length=4827813>
##contig=<ID=chr6_GL000251v2_alt,length=4795265>
##contig=<ID=chr6_GL000253v2_alt,length=4677643>
##contig=<ID=chr6_GL000250v2_alt,length=4672374>
##contig=<ID=chr6_GL000255v2_alt,length=4606388>
##contig=<ID=chr6_GL000252v2_alt,length=4604811>
##contig=<ID=chr17_KI270857v1_alt,length=2877074>
##contig=<ID=chr16_KI270853v1_alt,length=2659700>
##contig=<ID=chr16_KI270728v1_random,length=1872759>
##contig=<ID=chr17_GL000258v2_alt,length=1821992>
##contig=<ID=chr5_GL339449v2_alt,length=1612928>
##contig=<ID=chr14_KI270847v1_alt,length=1511111>
##contig=<ID=chr17_KI270908v1_alt,length=1423190>
##contig=<ID=chr14_KI270846v1_alt,length=1351393>
##contig=<ID=chr5_KI270897v1_alt,length=1144418>
##contig=<ID=chr7_KI270803v1_alt,length=1111570>
##contig=<ID=chr19_GL949749v2_alt,length=1091841>
##contig=<ID=chr19_KI270938v1_alt,length=1066800>
##contig=<ID=chr19_GL949750v2_alt,length=1066390>
##contig=<ID=chr19_GL949748v2_alt,length=1064304>
##contig=<ID=chr19_GL949751v2_alt,length=1002683>
##contig=<ID=chr19_GL949746v1_alt,length=987716>
##contig=<ID=chr19_GL949752v1_alt,length=987100>
##contig=<ID=chr8_KI270821v1_alt,length=985506>
##contig=<ID=chr1_KI270763v1_alt,length=911658>
##contig=<ID=chr6_KI270801v1_alt,length=870480>
##contig=<ID=chr19_GL949753v2_alt,length=796479>
##contig=<ID=chr19_GL949747v2_alt,length=729520>
##contig=<ID=chr8_KI270822v1_alt,length=624492>
##contig=<ID=chr4_GL000257v2_alt,length=586476>
##contig=<ID=chr12_KI270904v1_alt,length=572349>
##contig=<ID=chr4_KI270925v1_alt,length=555799>
##contig=<ID=chr15_KI270852v1_alt,length=478999>
##contig=<ID=chr15_KI270727v1_random,length=448248>
##contig=<ID=chr9_KI270823v1_alt,length=439082>
##contig=<ID=chr15_KI270850v1_alt,length=430880>
##contig=<ID=chr1_KI270759v1_alt,length=425601>
##contig=<ID=chr12_GL877876v1_alt,length=408271>
##contig=<ID=chrUn_KI270442v1,length=392061>
##contig=<ID=chr17_KI270862v1_alt,length=391357>
##contig=<ID=chr15_GL383555v2_alt,length=388773>
##contig=<ID=chr19_GL383573v1_alt,length=385657>
##contig=<ID=chr4_KI270896v1_alt,length=378547>
##contig=<ID=chr4_GL383528v1_alt,length=376187>
##contig=<ID=chr17_GL383563v3_alt,length=375691>
##contig=<ID=chr8_KI270810v1_alt,length=374415>
##contig=<ID=chr1_GL383520v2_alt,length=366580>
##contig=<ID=chr1_KI270762v1_alt,length=354444>
##contig=<ID=chr15_KI270848v1_alt,length=327382>
##contig=<ID=chr17_KI270909v1_alt,length=325800>
##contig=<ID=chr14_KI270844v1_alt,length=322166>
##contig=<ID=chr8_KI270900v1_alt,length=318687>
##contig=<ID=chr10_GL383546v1_alt,length=309802>
##contig=<ID=chr13_KI270838v1_alt,length=306913>
##contig=<ID=chr8_KI270816v1_alt,length=305841>
##contig=<ID=chr22_KI270879v1_alt,length=304135>
##contig=<ID=chr8_KI270813v1_alt,length=300230>
##contig=<ID=chr11_KI270831v1_alt,length=296895>
##contig=<ID=chr15_GL383554v1_alt,length=296527>
##contig=<ID=chr8_KI270811v1_alt,length=292436>
##contig=<ID=chr18_GL383567v1_alt,length=289831>
##contig=<ID=chrX_KI270880v1_alt,length=284869>
##contig=<ID=chr8_KI270812v1_alt,length=282736>
##contig=<ID=chr19_KI270921v1_alt,length=282224>
##contig=<ID=chr17_KI270729v1_random,length=280839>
##contig=<ID=chr17_JH159146v1_alt,length=278131>
##contig=<ID=chrX_KI270913v1_alt,length=274009>
##contig=<ID=chr6_KI270798v1_alt,length=271782>
##contig=<ID=chr7_KI270808v1_alt,length=271455>
##contig=<ID=chr22_KI270876v1_alt,length=263666>
##contig=<ID=chr15_KI270851v1_alt,length=263054>
##contig=<ID=chr22_KI270875v1_alt,length=259914>
##contig=<ID=chr1_KI270766v1_alt,length=256271>
##contig=<ID=chr19_KI270882v1_alt,length=248807>
##contig=<ID=chr3_KI270778v1_alt,length=248252>
##contig=<ID=chr15_KI270849v1_alt,length=244917>
##contig=<ID=chr4_KI270786v1_alt,length=244096>
##contig=<ID=chr12_KI270835v1_alt,length=238139>
##contig=<ID=chr17_KI270858v1_alt,length=235827>
##contig=<ID=chr19_KI270867v1_alt,length=233762>
##contig=<ID=chr16_KI270855v1_alt,length=232857>
##contig=<ID=chr8_KI270926v1_alt,length=229282>
##contig=<ID=chr5_GL949742v1_alt,length=226852>
##contig=<ID=chr3_KI270780v1_alt,length=224108>
##contig=<ID=chr17_GL383565v1_alt,length=223995>
##contig=<ID=chr2_KI270774v1_alt,length=223625>
##contig=<ID=chr4_KI270790v1_alt,length=220246>
##contig=<ID=chr11_KI270927v1_alt,length=218612>
##contig=<ID=chr19_KI270932v1_alt,length=215732>
##contig=<ID=chr11_KI270903v1_alt,length=214625>
##contig=<ID=chr2_KI270894v1_alt,length=214158>
##contig=<ID=chr14_GL000225v1_random,length=211173>
##contig=<ID=chrUn_KI270743v1,length=210658>
##contig=<ID=chr11_KI270832v1_alt,length=210133>
##contig=<ID=chr7_KI270805v1_alt,length=209988>
##contig=<ID=chr4_GL000008v2_random,length=209709>
##contig=<ID=chr7_KI270809v1_alt,length=209586>
##contig=<ID=chr19_KI270887v1_alt,length=209512>
##contig=<ID=chr4_KI270789v1_alt,length=205944>
##contig=<ID=chr3_KI270779v1_alt,length=205312>
##contig=<ID=chr19_KI270914v1_alt,length=205194>
##contig=<ID=chr19_KI270886v1_alt,length=204239>
##contig=<ID=chr11_KI270829v1_alt,length=204059>
##contig=<ID=chr14_GL000009v2_random,length=201709>
##contig=<ID=chr21_GL383579v2_alt,length=201197>
##contig=<ID=chr11_JH159136v1_alt,length=200998>
##contig=<ID=chr19_KI270930v1_alt,length=200773>
##contig=<ID=chrUn_KI270747v1,length=198735>
##contig=<ID=chr18_GL383571v1_alt,length=198278>
##contig=<ID=chr19_KI270920v1_alt,length=198005>
##contig=<ID=chr6_KI270797v1_alt,length=197536>
##contig=<ID=chr3_KI270935v1_alt,length=197351>
##contig=<ID=chr17_KI270861v1_alt,length=196688>
##contig=<ID=chr15_KI270906v1_alt,length=196384>
##contig=<ID=chr5_KI270791v1_alt,length=195710>
##contig=<ID=chr14_KI270722v1_random,length=194050>
##contig=<ID=chr16_GL383556v1_alt,length=192462>
##contig=<ID=chr13_KI270840v1_alt,length=191684>
##contig=<ID=chr14_GL000194v1_random,length=191469>
##contig=<ID=chr11_JH159137v1_alt,length=191409>
##contig=<ID=chr19_KI270917v1_alt,length=190932>
##contig=<ID=chr7_KI270899v1_alt,length=190869>
##contig=<ID=chr19_KI270923v1_alt,length=189352>
##contig=<ID=chr10_KI270825v1_alt,length=188315>
##contig=<ID=chr19_GL383576v1_alt,length=188024>
##contig=<ID=chr19_KI270922v1_alt,length=187935>
##contig=<ID=chrUn_KI270742v1,length=186739>
##contig=<ID=chr22_KI270878v1_alt,length=186262>
##contig=<ID=chr19_KI270929v1_alt,length=186203>
##contig=<ID=chr11_KI270826v1_alt,length=186169>
##contig=<ID=chr6_KB021644v2_alt,length=185823>
##contig=<ID=chr17_GL000205v2_random,length=185591>
##contig=<ID=chr1_KI270765v1_alt,length=185285>
##contig=<ID=chr19_KI270916v1_alt,length=184516>
##contig=<ID=chr19_KI270890v1_alt,length=184499>
##contig=<ID=chr3_KI270784v1_alt,length=184404>
##contig=<ID=chr12_GL383551v1_alt,length=184319>
##contig=<ID=chr20_KI270870v1_alt,length=183433>
##contig=<ID=chrUn_GL000195v1,length=182896>
##contig=<ID=chr1_GL383518v1_alt,length=182439>
##contig=<ID=chr22_KI270736v1_random,length=181920>
##contig=<ID=chr10_KI270824v1_alt,length=181496>
##contig=<ID=chr14_KI270845v1_alt,length=180703>
##contig=<ID=chr3_GL383526v1_alt,length=180671>
##contig=<ID=chr13_KI270839v1_alt,length=180306>
##contig=<ID=chr22_KI270733v1_random,length=179772>
##contig=<ID=chrUn_GL000224v1,length=179693>
##contig=<ID=chr10_GL383545v1_alt,length=179254>
##contig=<ID=chrUn_GL000219v1,length=179198>
##contig=<ID=chr5_KI270792v1_alt,length=179043>
##contig=<ID=chr17_KI270860v1_alt,length=178921>
##contig=<ID=chr19_GL000209v2_alt,length=177381>
##contig=<ID=chr11_KI270830v1_alt,length=177092>
##contig=<ID=chr9_KI270719v1_random,length=176845>
##contig=<ID=chrUn_GL000216v2,length=176608>
##contig=<ID=chr22_KI270928v1_alt,length=176103>
##contig=<ID=chr1_KI270712v1_random,length=176043>
##contig=<ID=chr6_KI270800v1_alt,length=175808>
##contig=<ID=chr1_KI270706v1_random,length=175055>
##contig=<ID=chr2_KI270776v1_alt,length=174166>
##contig=<ID=chr18_KI270912v1_alt,length=174061>
##contig=<ID=chr3_KI270777v1_alt,length=173649>
##contig=<ID=chr5_GL383531v1_alt,length=173459>
##contig=<ID=chr3_JH636055v2_alt,length=173151>
##contig=<ID=chr14_KI270725v1_random,length=172810>
##contig=<ID=chr5_KI270796v1_alt,length=172708>
##contig=<ID=chrEBV,length=171823>
##contig=<ID=chr9_GL383541v1_alt,length=171286>
##contig=<ID=chr19_KI270885v1_alt,length=171027>
##contig=<ID=chr19_KI270919v1_alt,length=170701>
##contig=<ID=chr19_KI270889v1_alt,length=170698>
##contig=<ID=chr19_KI270891v1_alt,length=170680>
##contig=<ID=chr19_KI270915v1_alt,length=170665>
##contig=<ID=chr19_KI270933v1_alt,length=170537>
##contig=<ID=chr19_KI270883v1_alt,length=170399>
##contig=<ID=chr19_GL383575v2_alt,length=170222>
##contig=<ID=chr19_KI270931v1_alt,length=170148>
##contig=<ID=chr12_GL383550v2_alt,length=169178>
##contig=<ID=chr13_KI270841v1_alt,length=169134>
##contig=<ID=chrUn_KI270744v1,length=168472>
##contig=<ID=chr18_KI270863v1_alt,length=167999>
##contig=<ID=chr18_GL383569v1_alt,length=167950>
##contig=<ID=chr12_GL877875v1_alt,length=167313>
##contig=<ID=chr21_KI270874v1_alt,length=166743>
##contig=<ID=chr3_KI270924v1_alt,length=166540>
##contig=<ID=chr1_KI270761v1_alt,length=165834>
##contig=<ID=chr3_KI270937v1_alt,length=165607>
##contig=<ID=chr22_KI270734v1_random,length=165050>
##contig=<ID=chr18_GL383570v1_alt,length=164789>
##contig=<ID=chr5_KI270794v1_alt,length=164558>
##contig=<ID=chr4_GL383527v1_alt,length=164536>
##contig=<ID=chrUn_GL000213v1,length=164239>
##contig=<ID=chr3_KI270936v1_alt,length=164170>
##contig=<ID=chr3_KI270934v1_alt,length=163458>
##contig=<ID=chr9_GL383539v1_alt,length=162988>
##contig=<ID=chr3_KI270895v1_alt,length=162896>
##contig=<ID=chr22_GL383582v2_alt,length=162811>
##contig=<ID=chr3_KI270782v1_alt,length=162429>
##contig=<ID=chr1_KI270892v1_alt,length=162212>
##contig=<ID=chrUn_GL000220v1,length=161802>
##contig=<ID=chr2_KI270767v1_alt,length=161578>
##contig=<ID=chr2_KI270715v1_random,length=161471>
##contig=<ID=chr2_KI270893v1_alt,length=161218>
##contig=<ID=chrUn_GL000218v1,length=161147>
##contig=<ID=chr18_GL383572v1_alt,length=159547>
##contig=<ID=chr8_KI270817v1_alt,length=158983>
##contig=<ID=chr4_KI270788v1_alt,length=158965>
##contig=<ID=chrUn_KI270749v1,length=158759>
##contig=<ID=chr7_KI270806v1_alt,length=158166>
##contig=<ID=chr7_KI270804v1_alt,length=157952>
##contig=<ID=chr18_KI270911v1_alt,length=157710>
##contig=<ID=chrUn_KI270741v1,length=157432>
##contig=<ID=chr17_KI270910v1_alt,length=157099>
##contig=<ID=chr19_KI270884v1_alt,length=157053>
##contig=<ID=chr19_GL383574v1_alt,length=155864>
##contig=<ID=chr19_KI270888v1_alt,length=155532>
##contig=<ID=chr3_GL000221v1_random,length=155397>
##contig=<ID=chr11_GL383547v1_alt,length=154407>
##contig=<ID=chr2_KI270716v1_random,length=153799>
##contig=<ID=chr12_GL383553v2_alt,length=152874>
##contig=<ID=chr6_KI270799v1_alt,length=152148>
##contig=<ID=chr22_KI270731v1_random,length=150754>
##contig=<ID=chrUn_KI270751v1,length=150742>
##contig=<ID=chrUn_KI270750v1,length=148850>
##contig=<ID=chr8_KI270818v1_alt,length=145606>
##contig=<ID=chrX_KI270881v1_alt,length=144206>
##contig=<ID=chr21_KI270873v1_alt,length=143900>
##contig=<ID=chr2_GL383521v1_alt,length=143390>
##contig=<ID=chr8_KI270814v1_alt,length=141812>
##contig=<ID=chr12_GL383552v1_alt,length=138655>
##contig=<ID=chrUn_KI270519v1,length=138126>
##contig=<ID=chr2_KI270775v1_alt,length=138019>
##contig=<ID=chr17_KI270907v1_alt,length=137721>
##contig=<ID=chrUn_GL000214v1,length=137718>
##contig=<ID=chr8_KI270901v1_alt,length=136959>
##contig=<ID=chr2_KI270770v1_alt,length=136240>
##contig=<ID=chr16_KI270854v1_alt,length=134193>
##contig=<ID=chr8_KI270819v1_alt,length=133535>
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