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Merge 726f0bc into 012e66e
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@ramprasadn
ramprasadn committed Apr 17, 2021
2 parents 012e66e + 726f0bc commit 6a757a1
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Showing 8 changed files with 43 additions and 17 deletions.
4 changes: 2 additions & 2 deletions lib/MIP/Program/Bcftools.pm
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Expand Up @@ -1265,7 +1265,7 @@ sub bcftools_norm {

if ($atom_overlaps) {

push @commands, q{--atom_overlaps} . $SPACE . $atom_overlaps;
push @commands, q{--atom-overlaps} . $SPACE . $atom_overlaps;
}

if ($multiallelic) {
Expand All @@ -1275,7 +1275,7 @@ sub bcftools_norm {

if ($old_rec_tag) {

push @commands, q{--old-rec-tag};
push @commands, q{--old-rec-tag OLD_REC_TAG};
}

if ($reference_check) {
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4 changes: 3 additions & 1 deletion lib/MIP/Recipes/Analysis/Bcftools_core.pm
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Expand Up @@ -237,9 +237,11 @@ sub analysis_bcftools_core {

bcftools_norm(
{

atomize => 1,
atom_overlaps => $DOT,
filehandle => $filehandle,
infile_path => q{-},
old_rec_tag => 1,
remove_duplicates => 1,
}
);
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11 changes: 7 additions & 4 deletions lib/MIP/Recipes/Analysis/Expansionhunter.pm
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Expand Up @@ -337,10 +337,13 @@ sub analysis_expansionhunter {
say {$filehandle} $NEWLINE;
bcftools_norm(
{
filehandle => $filehandle,
infile_path => $decompose_infile_path_prefix . q{.bcf},
multiallelic => q{-},
outfile_path => $decompose_outfile_path,
atomize => 1,
atom_overlaps => $DOT,
filehandle => $filehandle,
infile_path => $decompose_infile_path_prefix . q{.bcf},
multiallelic => q{-},
old_rec_tag => 1,
outfile_path => $decompose_outfile_path,
}
);
say {$filehandle} $NEWLINE;
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3 changes: 3 additions & 0 deletions lib/MIP/Recipes/Analysis/Gatk_cnnscorevariants.pm
View file
Expand Up @@ -277,9 +277,12 @@ sub analysis_gatk_cnnscorevariants {
$mv_infile_path = $norm_outfile_path;
bcftools_norm(
{
atomize => 1,
atom_overlaps => $DOT,
filehandle => $filehandle,
infile_path => $cnn_outfile_path,
multiallelic => $DASH,
old_rec_tag => 1,
outfile_path => $norm_outfile_path,
output_type => q{v},
reference_path => $referencefile_path,
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9 changes: 9 additions & 0 deletions lib/MIP/Recipes/Analysis/Gatk_variantrecalibration.pm
View file
Expand Up @@ -336,9 +336,12 @@ sub analysis_gatk_variantrecalibration_wes {
$outfile_path_prefix . $UNDERSCORE . q{normalized} . $outfile_suffix;
bcftools_norm(
{
atomize => 1,
atom_overlaps => $DOT,
filehandle => $filehandle,
infile_path => $norm_infile_path,
multiallelic => $DASH,
old_rec_tag => 1,
outfile_path => $norm_outfile_path,
output_type => q{v},
reference_path => $referencefile_path,
Expand Down Expand Up @@ -420,9 +423,12 @@ sub analysis_gatk_variantrecalibration_wes {
$outfile_path_prefix . $UNDERSCORE . q{selected_normalized} . $outfile_suffix;
bcftools_norm(
{
atomize => 1,
atom_overlaps => $DOT,
filehandle => $filehandle,
infile_path => $outfile_path,
multiallelic => $DASH,
old_rec_tag => 1,
outfile_path => $selected_norm_outfile_path,
output_type => q{v},
reference_path => $referencefile_path,
Expand Down Expand Up @@ -884,9 +890,12 @@ sub analysis_gatk_variantrecalibration_wgs {
$outfile_path_prefix . $UNDERSCORE . q{normalized} . $outfile_suffix;
bcftools_norm(
{
atomize => 1,
atom_overlaps => $DOT,
filehandle => $filehandle,
infile_path => $outfile_path,
multiallelic => $DASH,
old_rec_tag => 1,
output_type => q{v},
outfile_path => $bcftools_outfile_path,
reference_path => $referencefile_path,
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3 changes: 3 additions & 0 deletions lib/MIP/Recipes/Analysis/Plink.pm
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Expand Up @@ -316,8 +316,11 @@ sub analysis_plink {
my $uniq_outfile_path = $outfile_path_prefix . $UNDERSCORE . q{no_indels_ann_uniq.vcf};
bcftools_norm(
{
atomize => 1,
atom_overlaps => $DOT,
filehandle => $filehandle,
infile_path => $DASH,
old_rec_tag => 1,
outfile_path => $uniq_outfile_path,
remove_duplicates => 1,
}
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22 changes: 14 additions & 8 deletions lib/MIP/Recipes/Analysis/Sv_combinevariantcallsets.pm
View file
Expand Up @@ -299,10 +299,13 @@ sub analysis_sv_combinevariantcallsets {
say {$filehandle} q{## Split multiallelic variants};
bcftools_norm(
{
filehandle => $filehandle,
infile_path => $outfile_path,
multiallelic => q{-},
outfile_path => $outfile_path_prefix . $alt_file_tag . $outfile_suffix,
atomize => 1,
atom_overlaps => $DOT,
filehandle => $filehandle,
infile_path => $outfile_path,
multiallelic => q{-},
old_rec_tag => 1,
outfile_path => $outfile_path_prefix . $alt_file_tag . $outfile_suffix,
}
);
say {$filehandle} $NEWLINE;
Expand Down Expand Up @@ -579,10 +582,13 @@ sub _preprocess_joint_callers_file {
say {$filehandle} q{## Split multiallelic variants};
bcftools_norm(
{
filehandle => $filehandle,
infile_path => $infile_path,
multiallelic => q{-},
outfile_path => $decompose_outfile_path,
atomize => 1,
atom_overlaps => $DOT,
filehandle => $filehandle,
infile_path => $infile_path,
multiallelic => q{-},
old_rec_tag => 1,
outfile_path => $decompose_outfile_path,
}
);
say {$filehandle} $NEWLINE;
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4 changes: 2 additions & 2 deletions t/bcftools_norm.t
View file
Expand Up @@ -86,7 +86,7 @@ my %specific_argument = (
},
atom_overlaps => {
input => $BACKWARD_SLASH . $ASTERISK,
expected_output => q{--atom_overlaps} . $SPACE . $BACKWARD_SLASH . $ASTERISK,
expected_output => q{--atom-overlaps} . $SPACE . $BACKWARD_SLASH . $ASTERISK,
},
infile_path => {
input => q{infile.test},
Expand All @@ -98,7 +98,7 @@ my %specific_argument = (
},
old_rec_tag => {
input => 1,
expected_output => q{--old-rec-tag},
expected_output => q{--old-rec-tag OLD_REC_TAG},
},
output_type => {
input => q{v},
Expand Down

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