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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +1,31 @@ | ||
| ################## BASE IMAGE ###################### | ||
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| FROM clinicalgenomics/mip_base:2.1 | ||
| FROM ubuntu:bionic | ||
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| ################## METADATA ###################### | ||
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| LABEL base_image="clinicalgenomics/mip_base:2.1" | ||
| LABEL version="3" | ||
| LABEL software="expansionhunter" | ||
| LABEL software.version="4.0.2" | ||
| LABEL extra.binaries="expansionhunter" | ||
| LABEL base_image="ubuntu:bionic" | ||
| LABEL version="4" | ||
| LABEL software="ExpanionHunter" | ||
| LABEL software.version="5.0.0" | ||
| LABEL extra.binaries="ExpanionHunter" | ||
| LABEL maintainer="Clinical-Genomics/MIP" | ||
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| RUN conda install -c bioconda expansionhunter=4.0.2 | ||
| ## Install wget | ||
| RUN apt-get update && \ | ||
| apt-get install -y --no-install-recommends \ | ||
| ca-certificates \ | ||
| curl \ | ||
| wget \ | ||
| libreadline-dev && \ | ||
| apt-get clean && \ | ||
| apt-get purge && \ | ||
| rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* | ||
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| ## Clean up after conda | ||
| RUN /opt/conda/bin/conda clean -ya | ||
| WORKDIR /app | ||
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| WORKDIR /data/ | ||
| RUN wget -nv https://github.com/Illumina/ExpansionHunter/releases/download/v5.0.0/ExpansionHunter-v5.0.0-linux_x86_64.tar.gz && \ | ||
| tar -xvf ExpansionHunter-v5.0.0-linux_x86_64.tar.gz && \ | ||
| rm ExpansionHunter-v5.0.0-linux_x86_64.tar.gz | ||
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| ENV PATH=/app/ExpansionHunter-v5.0.0-linux_x86_64/bin:${PATH} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| # syntax=docker/dockerfile:1 | ||
| FROM clinicalgenomics/htslib:1.13 | ||
| WORKDIR /bin | ||
| COPY . . |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,131 @@ | ||
| #!/usr/bin/env perl | ||
| use strict; | ||
| use warnings; | ||
| use Data::Dumper; | ||
| use List::Util qw(sum); | ||
| use File::Basename qw(dirname); | ||
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| if ( $ARGV[0] eq "--version" ) { | ||
| print "generate_gens_data.pl 1.0.2\n"; | ||
| exit 0; | ||
| } | ||
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| my $SCRIPT_ROOT = dirname($0); | ||
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| my @COV_WINDOW_SIZES = ( 100000, 25000, 5000, 1000, 100 ); | ||
| my @BAF_SKIP_N = ( 160, 40, 10, 4, 1 ); | ||
| my @PREFIXES = qw( o a b c d ); | ||
| my $cov_fn = $ARGV[0]; | ||
| my $gvcf_fn = $ARGV[1]; | ||
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| my $SAMPLE_ID = $ARGV[2]; | ||
| my $GNOMAD = $ARGV[3]; | ||
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| my $COV_OUTPUT = $SAMPLE_ID . ".cov.bed"; | ||
| my $BAF_OUTPUT = $SAMPLE_ID . ".baf.bed"; | ||
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| print STDERR "Calculating coverage data\n"; | ||
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| # Calculate coverage data | ||
| open( COVOUT, ">" . $COV_OUTPUT ); | ||
| for my $i ( 0 .. $#COV_WINDOW_SIZES ) { | ||
| generate_cov_bed( $cov_fn, $COV_WINDOW_SIZES[$i], $PREFIXES[$i] ); | ||
| } | ||
| close COVOUT; | ||
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| print STDERR "Calculating BAFs from gvcf...\n"; | ||
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| # Calculate BAFs | ||
| system( $SCRIPT_ROOT. "/gvcfvaf.pl " . "$gvcf_fn $GNOMAD > baf.tmp" ); | ||
| open( BAFOUT, ">" . $BAF_OUTPUT ); | ||
| for my $i ( 0 .. $#BAF_SKIP_N ) { | ||
| print STDERR "Outputting BAF $PREFIXES[$i]...\n"; | ||
| generate_baf_bed( "baf.tmp", $BAF_SKIP_N[$i], $PREFIXES[$i] ); | ||
| } | ||
| close BAFOUT; | ||
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| system("bgzip -f -\@10 $BAF_OUTPUT"); | ||
| system("tabix -f -p bed $BAF_OUTPUT.gz"); | ||
| system("bgzip -f -\@10 $COV_OUTPUT"); | ||
| system("tabix -f -p bed $COV_OUTPUT.gz"); | ||
| unlink("baf.tmp"); | ||
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| sub generate_baf_bed { | ||
| my ( $fn, $skip, $prefix ) = @_; | ||
| open( my $fh, $fn ); | ||
| my $i = 0; | ||
| while (<$fh>) { | ||
| if ( $i++ % $skip == 0 ) { | ||
| chomp; | ||
| my @a = split /\t/; | ||
| print BAFOUT $prefix . "_" | ||
| . $a[0] . "\t" | ||
| . ( $a[1] - 1 ) . "\t" | ||
| . $a[1] . "\t" | ||
| . $a[2] . "\n"; | ||
| } | ||
| } | ||
| close $fh; | ||
| } | ||
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| sub generate_cov_bed { | ||
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| my ( $fn, $win_size, $prefix ) = @_; | ||
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| open( my $fh, $fn ); | ||
| my ( $reg_start, $reg_end, $reg_chr, $force_end ); | ||
| my @reg_ratios; | ||
| while (<$fh>) { | ||
| next if /^@/ or /^CONTIG/; | ||
| chomp; | ||
| my ( $chr, $start, $end, $ratio ) = split /\t/; | ||
| my $orig_end = $end; | ||
| unless ($reg_start) { | ||
| $reg_start = $start; | ||
| $reg_end = $end; | ||
| $reg_chr = $chr; | ||
| } | ||
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| if ( $chr eq $reg_chr ) { | ||
| if ( $start - $reg_end < $win_size ) { | ||
| push @reg_ratios, $ratio; | ||
| $reg_end = $end; | ||
| } | ||
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| # If there is a large gap to the next region, prematurely end region | ||
| else { | ||
| $force_end = 1; | ||
| $end = $reg_end; | ||
| } | ||
| } | ||
| else { | ||
| $force_end = 1; | ||
| $end = $reg_end; | ||
| } | ||
| if ( $end - $reg_start + 1 >= $win_size or $force_end ) { | ||
| my $mid_point = $reg_start + int( ( $end - $reg_start ) / 2 ); | ||
| print COVOUT $prefix . "_" | ||
| . $reg_chr . "\t" | ||
| . ( $mid_point - 1 ) . "\t" | ||
| . $mid_point . "\t" | ||
| . mean(@reg_ratios) . "\n"; | ||
| undef $reg_start; | ||
| undef $reg_end; | ||
| undef $reg_chr; | ||
| undef @reg_ratios; | ||
| } | ||
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| if ($force_end) { | ||
| $reg_start = $start; | ||
| $reg_end = $orig_end; | ||
| $reg_chr = $chr; | ||
| push @reg_ratios, $ratio; | ||
| undef $force_end; | ||
| } | ||
| } | ||
| close $fh; | ||
| } | ||
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| sub mean { | ||
| return sum(@_) / @_; | ||
| } |
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