| Previous changeset 11:ecbc563571ea (2016-12-12) Next changeset 13:02adb61c0246 (2017-01-18) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea |
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modified:
lumpy.xml test-data/output.vcf |
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added:
test-data/output_extended.vcf test-data/output_two.vcf |
| b |
| diff -r ecbc563571ea -r b3fb23bbca8e lumpy.xml --- a/lumpy.xml Mon Dec 12 13:45:08 2016 -0500 +++ b/lumpy.xml Sun Dec 18 10:35:43 2016 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="lumpy" name="lumpy-sv" version="0.2.1">\n+<tool id="lumpy" name="lumpy-sv" version="0.3.0">\n <description>find structural variants</description>\n <requirements>\n <requirement type="package" version="0.2.12">lumpy-sv</requirement>\n@@ -9,101 +9,76 @@\n <exit_code range="1:" level="fatal" description="Tool exception" />\n </stdio>\n <command detect_errors="exit_code"><![CDATA[\n+ #import re\n+ #set one_sample_bam = re.sub(\'[^\\w\\-]\', \'_\', str($analysis_type.input_file.element_identifier))\n #if $analysis_type.analysis_type_list == "one_sample":\n- ln -f -s \'$analysis_type.input_file\' input.bam &&\n+ ln -f -s \'$analysis_type.input_file\' \'$one_sample_bam\' &&\n #else:\n- ln -f -s \'$analysis_type.input_file\' input.A.bam &&\n- ln -f -s \'$analysis_type.input_fileB\' input.B.bam &&\n+ #set sample_a_bam = re.sub(\'[^\\w\\-]\', \'_\', str($analysis_type.input_file.element_identifier))\n+ #set sample_b_bam = re.sub(\'[^\\w\\-]\', \'_\', str($analysis_type.input_fileB.element_identifier))\n+ #if $sample_a_bam == $sample_b_bam:\n+ #set sample_a_bam = "%s_a" % str($sample_a_bam)\n+ #set sample_b_bam = "%s_b" % str($sample_b_bam)\n+ #end if\n+ ln -f -s \'$analysis_type.input_file\' \'$sample_a_bam\' &&\n+ ln -f -s \'$analysis_type.input_fileB\' \'$sample_b_bam\' &&\n #end if\n \n #if $analysis_type.analysis_type_list == "one_sample":\n \n #if $seq_method.seq_method_list == "paired-end":\n- samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" &&\n- samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&\n- samtools sort input.discordants.unsorted.bam > input.discordants.bam &&\n- samtools sort input.splitters.unsorted.bam > input.splitters.bam &&\n- samtools view input.bam\n- |tail -n +1\n+ samtools view -u -F 1294 \'$one_sample_bam\' | samtools sort -O bam -o input.discordants.bam &&\n+ samtools view -h \'$one_sample_bam\' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&\n+ samtools view \'$one_sample_bam\'\n |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&\n mean=\\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&\n stdev=\\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&\n- lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt\n+ lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt\n #if $output_format == "BEDPE":\n -b\n #end if\n- -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\\$mean",stdev:"\\$stdev",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold\n- -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&\n- mv input.discordants.bam $discordants &&\n- mv input.splitters.bam $splits &&\n- '..b'at="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution">\n+ <data format="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution" from_work_dir="input.lib.histo">\n <filter>seq_method[\'seq_method_list\'] == "paired-end"</filter>\n </data>\n- <data format="tabular" name="histogramB" label="Lumpy on ${on_string}: Fragment size distribution">\n+ <data format="tabular" name="histogramB" label="Lumpy on ${on_string}: Fragment size distribution" from_work_dir="input.B.lib.histo">\n <filter>seq_method[\'seq_method_list\'] == "paired-end"</filter>\n <filter>analysis_type[\'analysis_type_list\'] == "two_sample"</filter>\n </data>\n- <data format="bam" name="splits" label="Lumpy on ${on_string}: Split Reads (Bam format)"/>\n- <data format="bam" name="splitsB" label="Lumpy on ${on_string}: Split Reads (Bam format)">\n+ <data format="bam" name="splits" label="Lumpy on ${on_string}: Split Reads (Bam format)" from_work_dir="input.splitters.bam"/>\n+ <data format="bam" name="splitsB" label="Lumpy on ${on_string}: Split Reads (Bam format)" from_work_dir="input.B.splitters.bam">\n <filter>analysis_type[\'analysis_type_list\'] == "two_sample"</filter>\n </data>\n- <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)">\n+ <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.bam">\n <filter>seq_method[\'seq_method_list\'] == "paired-end"</filter>\n </data>\n- <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)">\n+ <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.B.bam">\n <filter>seq_method[\'seq_method_list\'] == "paired-end"</filter>\n <filter>analysis_type[\'analysis_type_list\'] == "two_sample"</filter>\n </data>\n@@ -187,7 +166,7 @@\n \n <tests>\n <test>\n- <param name="analysis_type" value="one_sample" />\n+ <param name="analysis_type_list" value="one_sample" />\n <param name="input_file" value="sr.input.bam" ftype="bam"/>\n <param name="seq_method_list" value="single-read" />\n <param name="mw" value="4"/>\n@@ -197,6 +176,31 @@\n <param name="min_mapping_threshold" value="20" />\n <output name="vcf_call" file="output.vcf" ftype="vcf"/>\n </test>\n+ <test>\n+ <param name="analysis_type_list" value="one_sample" />\n+ <param name="input_file" value="sr.input.bam" ftype="bam"/>\n+ <param name="seq_method_list" value="single-read" />\n+ <param name="mw" value="4"/>\n+ <param name="tt" value="0"/>\n+ <param name="back_distance" value="10"/>\n+ <param name="weight" value="1" />\n+ <param name="min_mapping_threshold" value="20" />\n+ <param name="evidence" value="true" />\n+ <param name="probability_curve" value="true" />\n+ <output name="vcf_call" file="output_extended.vcf" ftype="vcf" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="analysis_type_list" value="two_sample" />\n+ <param name="input_file" value="sr.input.bam" ftype="bam"/>\n+ <param name="input_fileB" value="sr.input.bam" ftype="bam"/>\n+ <param name="seq_method_list" value="single-read" />\n+ <param name="mw" value="4"/>\n+ <param name="tt" value="0"/>\n+ <param name="back_distance" value="10"/>\n+ <param name="weight" value="1" />\n+ <param name="min_mapping_threshold" value="20" />\n+ <output name="vcf_call" file="output_two.vcf" ftype="vcf"/>\n+ </test>\n </tests>\n \n <help>\n' |
| b |
| diff -r ecbc563571ea -r b3fb23bbca8e test-data/output.vcf --- a/test-data/output.vcf Mon Dec 12 13:45:08 2016 -0500 +++ b/test-data/output.vcf Sun Dec 18 10:35:43 2016 -0500 |
| [ |
| @@ -30,7 +30,7 @@ ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT input.bam +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sr_input_bam hg38_gold_U07000.1 14 1_1 N [hg38_gold_U07000.1:1876[N . . SVTYPE=BND;STRANDS=--:19;EVENT=1;MATEID=1_2;CIPOS=0,0;CIEND=0,2;CIPOS95=0,0;CIEND95=0,0;SU=19;SR=19 GT:SU:SR ./.:19:19 hg38_gold_U07000.1 1876 1_2 N [hg38_gold_U07000.1:14[N . . SVTYPE=BND;STRANDS=--:19;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=0,2;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=19;SR=19 GT:SU:SR ./.:19:19 hg38_gold_U07000.1 10 2_1 N [hg38_gold_U07000.1:1897[N . . SVTYPE=BND;STRANDS=--:19;EVENT=2;MATEID=2_2;CIPOS=-1,0;CIEND=-7,5;CIPOS95=0,1;CIEND95=-2,1;IMPRECISE;SU=19;SR=19 GT:SU:SR ./.:19:19 |
| b |
| diff -r ecbc563571ea -r b3fb23bbca8e test-data/output_extended.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_extended.vcf Sun Dec 18 10:35:43 2016 -0500 |
| [ |
| b'@@ -0,0 +1,75 @@\n+##fileformat=VCFv4.2\n+##source=LUMPY\n+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">\n+##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">\n+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">\n+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">\n+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">\n+##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">\n+##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">\n+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">\n+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">\n+##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">\n+##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">\n+##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">\n+##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">\n+##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">\n+##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">\n+##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">\n+##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">\n+##ALT=<ID=DEL,Description="Deletion">\n+##ALT=<ID=DUP,Description="Duplication">\n+##ALT=<ID=INV,Description="Inversion">\n+##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">\n+##ALT=<ID=INS,Description="Insertion of novel sequence">\n+##ALT=<ID=CNV,Description="Copy number variable region">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">\n+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">\n+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">\n+##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsr_input_bam\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:22421:6659_2\thg38_gold_U07000.1\t8\t50\thg38_gold_U07000.1\t1885\t1932\t0x17456f0\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:21503:6234_2\thg38_gold_U07000.1\t13\t52\thg38_gold_U07000.1\t1885\t1933\t0x17451d0\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:14108:4338_2\thg38_gold_U07000.1\t8\t53\thg38_gold_U07000.1\t1879\t1932\t0x1747410\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:22281:3587_2\thg38_gold_U07000.1\t8\t52\thg38_gold_U07000.1\t1879\t1944\t0x174d920\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:9129:3504_2\thg38_gold_U07000.1\t13\t50\thg38_gold_U07000.1\t1872\t1932\t0x1748e60\t0\t+\t-\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:10154:5887_2\thg38_gold_U07000.1\t10\t41\thg38_gold_U07000.1\t1872\t1931\t0x17499d0\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:9382:5932_2\thg38_gold_U07000.1\t8\t53\thg38_gold_U07000.1\t1871\t1921\t0x174d580\t0\t+\t-\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:22747:6442_2\thg38_gold_U07000.1\t8\t52\thg38_gold_U07000.1\t1870\t1933\t0x1748cc0'..b':1101:12490:4165_2\thg38_gold_U07000.1\t13\t58\thg38_gold_U07000.1\t1868\t1917\t0x174d9f0\t0\t-\t+\tid:1\tweight:1\n+hg38_gold_U07000.1\t14\t1_1\tN\t[hg38_gold_U07000.1:1876[N\t.\t.\tSVTYPE=BND;STRANDS=--:19;EVENT=1;MATEID=1_2;CIPOS=0,0;CIEND=0,2;CIPOS95=0,0;CIEND95=0,0;SU=19;SR=19;PRPOS=1;PREND=0.99996,3.98091e-05,1.58483e-09\tGT:SU:SR\t./.:19:19\n+hg38_gold_U07000.1\t1876\t1_2\tN\t[hg38_gold_U07000.1:14[N\t.\t.\tSVTYPE=BND;STRANDS=--:19;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=0,2;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=19;SR=19;PRPOS=0.99996,3.98091e-05,1.58483e-09;PREND=1\tGT:SU:SR\t./.:19:19\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:7043:5583_2\thg38_gold_U07000.1\t13\t56\thg38_gold_U07000.1\t1899\t1935\t0x1742010\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:19472:2185_2\thg38_gold_U07000.1\t0\t56\thg38_gold_U07000.1\t1898\t1945\t0x1744270\t0\t+\t-\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:9324:6462_2\thg38_gold_U07000.1\t0\t51\thg38_gold_U07000.1\t1898\t1933\t0x1748fd0\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:23764:6273_2\thg38_gold_U07000.1\t13\t48\thg38_gold_U07000.1\t1898\t1945\t0x17490a0\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:7772:5906_2\thg38_gold_U07000.1\t0\t54\thg38_gold_U07000.1\t1898\t1942\t0x1747240\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:6971:4906_2\thg38_gold_U07000.1\t13\t51\thg38_gold_U07000.1\t1898\t1935\t0x1746170\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:10511:4776_2\thg38_gold_U07000.1\t8\t50\thg38_gold_U07000.1\t1898\t1934\t0x174a840\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:19677:3538_2\thg38_gold_U07000.1\t13\t51\thg38_gold_U07000.1\t1898\t1940\t0x174c190\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:22109:4922_2\thg38_gold_U07000.1\t13\t53\thg38_gold_U07000.1\t1897\t1933\t0x1743ac0\t0\t+\t-\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:14027:4470_2\thg38_gold_U07000.1\t0\t51\thg38_gold_U07000.1\t1896\t1933\t0x174b500\t0\t+\t-\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:22736:5607_2\thg38_gold_U07000.1\t13\t57\thg38_gold_U07000.1\t1893\t1945\t0x174cf30\t0\t+\t-\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:10768:5508_2\thg38_gold_U07000.1\t13\t56\thg38_gold_U07000.1\t1893\t1935\t0x17480b0\t0\t+\t-\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:14449:3437_2\thg38_gold_U07000.1\t13\t48\thg38_gold_U07000.1\t1893\t1933\t0x174b150\t0\t+\t-\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:18009:3360_2\thg38_gold_U07000.1\t13\t47\thg38_gold_U07000.1\t1893\t1925\t0x1749390\t0\t+\t-\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:16615:6513_2\thg38_gold_U07000.1\t13\t51\thg38_gold_U07000.1\t1893\t1931\t0x174b860\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:19235:5076_2\thg38_gold_U07000.1\t13\t45\thg38_gold_U07000.1\t1893\t1932\t0x174a790\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:14629:4828_2\thg38_gold_U07000.1\t8\t50\thg38_gold_U07000.1\t1893\t1932\t0x174b360\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:22780:4994_2\thg38_gold_U07000.1\t13\t50\thg38_gold_U07000.1\t1892\t1924\t0x174aaf0\t0\t-\t+\tid:1\tweight:1\n+\tEvidence:\tM00860:26:000000000-A6UGV:1:1101:12387:3929_2\thg38_gold_U07000.1\t13\t51\thg38_gold_U07000.1\t1892\t1931\t0x174c000\t0\t-\t+\tid:1\tweight:1\n+hg38_gold_U07000.1\t10\t2_1\tN\t[hg38_gold_U07000.1:1897[N\t.\t.\tSVTYPE=BND;STRANDS=--:19;EVENT=2;MATEID=2_2;CIPOS=-1,0;CIEND=-7,5;CIPOS95=0,1;CIEND95=-2,1;IMPRECISE;SU=19;SR=19;PRPOS=9.99999e-13,9.99999e-07;PREND=4.89496e-31,1.94872e-23,7.75799e-16,3.08851e-08,0.0308851,0.0775799,0.194872,0.489496,0.194872,0.0122956,1.94872e-09,4.89496e-17,1.22956e-24\tGT:SU:SR\t./.:19:19\n+hg38_gold_U07000.1\t1897\t2_2\tN\t[hg38_gold_U07000.1:10[N\t.\t.\tSVTYPE=BND;STRANDS=--:19;SECONDARY;EVENT=2;MATEID=2_1;CIPOS=-7,5;CIEND=-1,0;CIPOS95=-2,1;CIEND95=0,1;IMPRECISE;SU=19;SR=19;PRPOS=4.89496e-31,1.94872e-23,7.75799e-16,3.08851e-08,0.0308851,0.0775799,0.194872,0.489496,0.194872,0.0122956,1.94872e-09,4.89496e-17,1.22956e-24;PREND=9.99999e-13,9.99999e-07\tGT:SU:SR\t./.:19:19\n' |
| b |
| diff -r ecbc563571ea -r b3fb23bbca8e test-data/output_two.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_two.vcf Sun Dec 18 10:35:43 2016 -0500 |
| [ |
| @@ -0,0 +1,37 @@ +##fileformat=VCFv4.2 +##source=LUMPY +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> +##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> +##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> +##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> +##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> +##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> +##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> +##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> +##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> +##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> +##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> +##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> +##ALT=<ID=DEL,Description="Deletion"> +##ALT=<ID=DUP,Description="Duplication"> +##ALT=<ID=INV,Description="Inversion"> +##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> +##ALT=<ID=INS,Description="Insertion of novel sequence"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> +##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> +##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> +##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sr_input_bam_a sr_input_bam_b +hg38_gold_U07000.1 14 1_1 N [hg38_gold_U07000.1:1876[N . . SVTYPE=BND;STRANDS=--:38;EVENT=1;MATEID=1_2;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=38;SR=38 GT:SU:SR ./.:19:19 ./.:19:19 +hg38_gold_U07000.1 1876 1_2 N [hg38_gold_U07000.1:14[N . . SVTYPE=BND;STRANDS=--:38;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=38;SR=38 GT:SU:SR ./.:19:19 ./.:19:19 +hg38_gold_U07000.1 10 2_1 N [hg38_gold_U07000.1:1897[N . . SVTYPE=BND;STRANDS=--:38;EVENT=2;MATEID=2_2;CIPOS=0,0;CIEND=-7,5;CIPOS95=0,1;CIEND95=-1,1;IMPRECISE;SU=38;SR=38 GT:SU:SR ./.:19:19 ./.:19:19 +hg38_gold_U07000.1 1897 2_2 N [hg38_gold_U07000.1:10[N . . SVTYPE=BND;STRANDS=--:38;SECONDARY;EVENT=2;MATEID=2_1;CIPOS=-7,5;CIEND=0,0;CIPOS95=-1,1;CIEND95=0,1;IMPRECISE;SU=38;SR=38 GT:SU:SR ./.:19:19 ./.:19:19 |