| Next changeset 1:021a0f7ab3f6 (2016-05-20) |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 1f1c277219ca756c9baa453592b455597fd593d8-dirty |
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README breakdancer.xml create_config_file.py test-data/README test-data/X_10000000_Hum1.bam test-data/X_10000000_Hum1.bed |
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| diff -r 000000000000 -r f65530d07350 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue May 17 04:35:44 2016 -0400 |
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| b'@@ -0,0 +1,162 @@\n+BreakDancer-1.3.6, released under GPLv3, is a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs. Please read our paper for detailed algorithmic description. http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html\r\n+\r\n+BreakDancerMax (Update from 1.0 to 1.1 version only applied to cpp now.)\r\n+----------------------\r\n+Usage: breakdancer_max <analysis_config_file>\r\n+Options:\r\n+ -o STRING operate on a single chromosome [all chromosome]\n+ -s INT minimum length of a region [7]\n+ -c INT cutoff in unit of standard deviation [3]\n+ -m INT maximum SV size [1000000000]\n+ -q INT minimum alternative mapping quality [35]\n+ -r INT minimum number of read pairs required to establish a connection [2]\n+ -x INT maximum threshold of haploid sequence coverage for regions to be ignored [1000]\n+ -b INT buffer size for building connection [100]\n+ -t only detect transchromosomal rearrangement, by default off\n+ -d STRING prefix of fastq files that SV supporting reads will be saved by library\n+ -g STRING dump SVs and supporting reads in BED format for GBrowse\n+ -l analyze Illumina long insert (mate-pair) library\n+ -a print out copy number by bam file rather than library, by default on\n+ -h print out Allele Frequency column, by default off\n+ -y INT output score filter [40]\r\n+\n+The followings are the new functions of version 1.1 from 1.0:\n+\n+1. It computes the copy number based on the normalization of the whole genome or whole chromosome along with the SV detection. By default the copy number is computed by bam file, but it can also compute per library with option "-a".\n+2. The Allele Frequency column is more accurate for DEL type, with the help of the copy number computation. By default it is off. Include option "-h" if you want to look at the DEL type Allele Frequency.\n+3. Since there are numerous false positive SV calls, the output has a cutoff of the PhredQ score, which by default is 40. Make sure to use option "-y yournumber" if you want to change the cutoff.\n+\n+The followings are those existing in version 1.0:\n+\r\n+Most of these options are self-explanatory. It is convenient to use the -o option to parallelize SV detection for each chromosome. When -o is used, the detection of inter-chromosomal translocation is disabled. In that case, it may be convenient to use -t in a separate process to detect putative inter-chromosomal translocations without bothering to analyze read pairs that are mapped to the same chromosome. \r\n+\r\n+The beta-test x86_64 Cpp version breakdancermax directly utilizes samtools C library. It is fully compatible with the perl version with identical usage and functions but is over 10 times faster. However, it only supports properly formated bam files and has only been tested using bam files produced by BWA. To obtain the correct result, it is important to have readgroup (@RG) tag in both the header and each alignment in the bam files. If you experience technical difficulty with the Cpp version, please email breakdancer-help@lists.sourceforge.net or consider using the perl version.\r\n+\r\n+The input to BreakDancerMax-1.1 is a set of map files produced by a front-end aligner such as MAQ, BWA, NovoAlign and Bfast, and a tab-delimited configuration file that specifies the locations of th'..b'here all SV supporting reads will be saved in the fastq format. These reads can be realigned by other aligners such as novoalign, and then reanalyzed by BreakDancer.\r\n+\r\n+Listing multiple map files in a single configuration file would automatically enable pooled analysis: reads from all the map files are jointly analyzed to find unified SV hypotheses across all the map files.\r\n+\r\n+\r\n+The output format\r\n+----------------------\r\n+BreakDancer\'s output file consists of the following columns:\r\n+\r\n+1. Chromosome 1\r\n+2. Position 1\r\n+3. Orientation 1\r\n+4. Chromosome 2\r\n+5. Position 2\r\n+6. Orientation 2\r\n+7. Type of a SV\r\n+8. Size of a SV\r\n+9. Confidence Score\r\n+10. Total number of supporting read pairs\r\n+11. Total number of supporting read pairs from each map file\r\n+12. Estimated allele frequency\r\n+13. Software version\r\n+14. The run parameters\r\n+\r\n+Columns 1-3 and 4-6 are used to specify the coordinates of the two SV breakpoints. The orientation is a string that records the number of reads mapped to the plus (+) or the minus (-) strand in the anchoring regions.\r\n+\r\n+Column 7 is the type of SV detected: DEL (deletions), INS (insertion), INV (inversion), ITX (intra-chromosomal translocation), CTX (inter-chromosomal translocation), and Unknown. \r\n+Column 8 is the size of the SV in bp. It is meaningless for inter-chromosomal translocations. \r\n+Column 9 is the confidence score associated with the prediction. \r\n+Column 11 can be used to dissect the origin of the supporting read pairs, which is useful in pooled analysis. For example, one may want to give SVs that are supported by more than one libraries higher confidence than those detected in only one library. It can also be used to distinguish somatic events from the germline, i.e., those detected in only the tumor libraries versus those detected in both the tumor and the normal libraries.\r\n+Column 12 is currently a placeholder for displaying estimated allele frequency. The allele frequencies estimated in this version are not accurate and should not be trusted.\r\n+Column 13 and 14 are information useful to reproduce the results.\r\n+\r\n+Example 1:\r\n+1 10000 10+0- 2 20000 7+10- CTX -296 99 10 tB|10 1.00 BreakDancerMax-0.0.1 t1\r\n+\r\n+An inter-chromosomal translocation that starts from chr1:10000 and goes into chr2:20000 with 10 supporting read pairs from the library tB and a confidence score of 99.\r\n+\r\n+Example 2:\r\n+1 59257 5+1- 1 60164 0+5- DEL 862 99 5 nA|2:tB|1 0.56 BreakDancerMax-0.0.1 c4\r\n+\r\n+A deletion between chr1:59257 and chr1:60164 connected by 5 read pairs, among which 2 in library nA and 1 in library tB support the deletion hypothesis. This deletion is detected by BreakDancerMax-0.0.1 with a separation threshold of 4 s.d.\r\n+\r\n+Example 3:\r\n+1 62767 10+0- 1 63126 0+10- INS -13 36 10 NA|10 1.00 BreakDancerMini-0.0.1 q10\r\n+\r\n+An 13 bp insertion detected by BreakDancerMini between chr1:62767 and chr1:63126 with 10 supporting read pairs from a single library \'NA\' and a confidence score of 36.\r\n+\r\n+Notes:\r\n+Real SV breakpoints are expected to reside within the predicted boundaries with a margin > the read length.\r\n+\r\n+The BreakDancerMini code will not be included in the coming releases. We recommend using Pindel to detect intermediate size indels (10-80 bp).\r\n+\r\n+Dependence over other Perl Modules\r\n+------------------------------------\r\n+use Statistics::Descriptive;\r\n+use Math::CDF;\r\n+\r\n+These are available at CPAN.\r\n+http://search.cpan.org/~colink/Statistics-Descriptive-2.6/Descriptive.pm\r\n+http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm\r\n+\r\n+use Poisson;\r\n+This is provided. Please make sure the "use lib" at the beginning of the perl scripts contains the correct path.\r\n+\r\n+\r\n+Acknowledgements\r\n+-----------------\r\n+Heng Li at Wellcome Trust Sanger Institute has contributed an early version of this code.\r\n+Many colleagues at The Genome Center of Washington University have supported this effort.\r\n+\r\n+\r\n+Ken Chen and Xian Fan\r\n+Washington University Genome Center\r\n+\r\n+July 14, 2009\r\n' |
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| diff -r 000000000000 -r f65530d07350 breakdancer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/breakdancer.xml Tue May 17 04:35:44 2016 -0400 |
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| b'@@ -0,0 +1,177 @@\n+<tool id="breakdancer_max" name="BreakdancerMax" version="1.3.6">\n+ <description></description>\n+ <requirements>\n+ <requirement type="package" version="0.1.19">samtools</requirement>\n+ <requirement type="package" version="1.4.5">breakdancer</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command><![CDATA[\n+ ln -f -s "$input_file.metadata.bam_index" alignment.bam.bai &&\n+ ln -f -s "$input_file" alignment.bam &&\n+ python $__tool_directory__/create_config_file.py\n+ --input_file alignment.bam\n+ --mean "$mean"\n+ --std_dev "$std_dev"\n+ --read_length "$read_length"\n+ --sample_name "$sample_name"\n+ --output_config_file output_config_file &&\n+ cat output_config_file &&\n+ breakdancer-max\n+ -s "$min_length"\n+ -c "$cutoff"\n+ -m "$maximum_sv"\n+ -q "$quality"\n+ -r "$min_rp"\n+ -x "$hap_seq_threshold"\n+ -b "$buffer_size"\n+ $transchr_rearr\n+ -d "$sample_name"\n+ -g "$sample_name"\n+ $illumina_long\n+ $copy_number_bam\n+ $allele_freq\n+ -y "$output_score_filter"\n+ output_config_file &&\n+ mv "$sample_name" "$results_bed"\n+ ]]></command>\n+ <inputs>\n+ <param name="input_file" type="data" format="bam" label="One or more alignment files"/>\n+ <param name="mean" type="integer" value="" label="Mean Insert Size"/>\n+ <param name="std_dev" type="integer" value="" label="The standard deviation of insert size"/>\n+ <param name="read_length" type="integer" value="" label="Average read length"/>\n+ <param name="sample_name" type="text" label="Sample name"/>\n+ <param name="min_length" type="integer" value="7"\n+ label="Minimal required size of a SV anchoring region from which the anomalously mapped reads are found"/>\n+ <param name="cutoff" type="integer" value="3" label="Cutoff in unit of standard deviation"/>\n+ <param name="maximum_sv" type="integer" value="1000000000" label="Maximum SV Size"/>\n+ <param name="quality" type="integer" value="35" label="Minimum MAQ mapping quality threshold"/>\n+ <param name="min_rp" type="integer" value="2"\n+ label="Minimum number of read pairs required to establish a connection"/>\n+ <param name="hap_seq_threshold" type="integer" value="1000"\n+ label="Maximum threshold of haploid sequence coverage for regions to be ignored"/>\n+ <param name="buffer_size" type="integer" value="100"\n+ label="Buffer size for building connection"/>\n+ <param name="transchr_rearr" type="boolean" checked="false" truevalue="-t" falsevalue=""\n+ label="Only detect transchromosomal rearrangement (Default = No)"/>\n+ <param name="illumina_long" type="boolean" checked="false" truevalue="-l" falsevalue=""\n+ label="Analyze Illumina long insert (mate-pair) library"/>\n+ <param name="copy_number_bam" type="boolean" checked="false" truevalue="-a" falsevalue=""\n+ label="Compute copy number and support reads per library rather than per bam (Default = No)"/>\n+ <param name="allele_freq" type="boolean" checked="false" truevalue="-h" falsevalue=""\n+ label="Print out Allele Frequencing column (Default= No)"/>\n+ <param name="output_score_filter" type="integer" value="30" label="Output Score filter"/>\n+ </inputs>\n+ <outputs>\n+ <data name="results_bed" type="data" format="bed" help="BED file containing SVs and supporting reads" label="${sample_name}"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_file" value="X_Hum1.bwa.bam" ftype="bam"/>\n+ <param name="mean" value="227"/>\n+ <param name="std_dev" value="98"/>\n+ <param name="read_length" value="125"/>\n+ <param name="sample_name" value='..b'respectively. It is useful to explicitly specify the upper and the lower separation thresholds when the insert size distribution is not symmetric to the mean.\n+- Maximum SV size. (Default = 1000000000)\n+- Minimum MAQ mapping quality threshold. Can be used to skip reads that are not confidently mapped. (Default = 35)\n+- Minimum number of read pairs required to establish a connection. (Default = 2)\n+- Maximum threshold of haploid sequence coverage for regions to be ignored. (Default = 1000)\n+- Buffer size for building connection. The -b parameter specifies the number of anomalous regions resides in the RAM before SV hypotheses begin to form among these regions. For dataset that is exceptionally large, it may be helpful to reduce it to cut the resident RAM usage. (Default = 100)\n+- Only detect transchromosomal rearrangement. (Default = off)\n+- Prefix of fastq files to which SV supporting reads will be saved to, by library\n+- Analyze Illumina long insert (mate-pair) library (Default = off)\n+- Compute copy number by bam file rather than by library (Default = on)\n+- Print out Allele Frequencing column (Default = off)\n+- Output Score filter (Default = 40)\n+\n+Output files\n+------------\n+BreakDancer output is a BED file containing SVs and supporting reads. It has the following columns:\n+1. Chromosome 1\n+2. Position 1\n+3. Orientation 1\n+4. Chromosome 2\n+5. Position 2\n+6. Orientation 2\n+7. Type of a SV\n+8. Size of a SV\n+9. Confidence Score\n+10. Total number of supporting read pairs\n+11. Total number of supporting read pairs from each map file\n+12. Estimated allele frequency\n+13. Software version\n+14. The run parameters\n+\n+Columns 1-3 and 4-6 are used to specify the coordinates of the two SV breakpoints. The orientation is a string that records the number of reads mapped to the plus (+) or the minus (-) strand in the anchoring regions.\n+\n+Column 7 is the type of SV detected: DEL (deletions), INS (insertion), INV (inversion), ITX (intra-chromosomal translocation), CTX (inter-chromosomal translocation), and Unknown.\n+Column 8 is the size of the SV in bp. It is meaningless for inter-chromosomal translocations.\n+Column 9 is the confidence score associated with the prediction.\n+Column 11 can be used to dissect the origin of the supporting read pairs, which is useful in pooled analysis. For example, one may want to give SVs that are supported by more than one libraries higher confidence than those detected in only one library. It can also be used to distinguish somatic events from the germline, i.e., those detected in only the tumor libraries versus those detected in both the tumor and the normal libraries.\n+Column 12 is currently a placeholder for displaying estimated allele frequency. The allele frequencies estimated in this version are not accurate and should not be trusted.\n+Column 13 and 14 are information useful to reproduce the results.\n+\n+Example 1:\n+1 10000 10+0- 2 20000 7+10- CTX -296 99 10 tB|10 1.00 BreakDancerMax-0.0.1 t1\n+\n+An inter-chromosomal translocation that starts from chr1:10000 and goes into chr2:20000 with 10 supporting read pairs from the library tB and a confidence score of 99.\n+\n+Example 2:\n+1 59257 5+1- 1 60164 0+5- DEL 862 99 5 nA|2:tB|1 0.56 BreakDancerMax-0.0.1 c4\n+\n+A deletion between chr1:59257 and chr1:60164 connected by 5 read pairs, among which 2 in library nA and 1 in library tB support the deletion hypothesis. This deletion is detected by BreakDancerMax-0.0.1 with a separation threshold of 4 s.d.\n+\n+Example 3:\n+1 62767 10+0- 1 63126 0+10- INS -13 36 10 NA|10 1.00 BreakDancerMini-0.0.1 q10\n+\n+An 13 bp insertion detected by BreakDancerMini between chr1:62767 and chr1:63126 with 10 supporting read pairs from a single library \'NA\' and a confidence score of 36.\n+\n+Notes:\n+Real SV breakpoints are expected to reside within the predicted boundaries with a margin > the read length.\n+\n+\n+\n+ ]]> </help>\n+ <citations>\n+ <citation type="doi">doi:10.1038/nmeth.1363</citation>\n+ </citations>\n+</tool>\n+\n' |
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| diff -r 000000000000 -r f65530d07350 create_config_file.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_config_file.py Tue May 17 04:35:44 2016 -0400 |
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| @@ -0,0 +1,21 @@ +import argparse + + +description = ("This script will create a configuration file for samples to be run in Breakdancer." + "If pooled analysis desired, only one config file needed for all samples." + "Otherwise, individual analysis requires individual config files for each sample.") + +parser = argparse.ArgumentParser() +parser.add_argument("--input_file", nargs="*", help="One or more alignment files") +parser.add_argument("--mean", nargs="+", help="Mean insert size") +parser.add_argument("--std_dev", nargs="+", help="The standard deviation of insert size") +parser.add_argument("--read_length", nargs="+", help="Average read length") +parser.add_argument("--sample_name", nargs="+", help="Sample name") +parser.add_argument("--output_config_file", help="Name of the output config file") +args = parser.parse_args() + +template = "map:{input_file}\tmean:{mean}\tstd:{std_dev}\treadlen:{read_length}\tsample:{sample_name}\texe:samtools view\n" +with open(args.output_config_file, "w") as output: + for input_file, mean, std_dev, read_length, sample_name in zip(args.input_file, args.mean, args.std_dev, args.read_length, args.sample_name): + config_line = template.format(input_file=input_file, mean=mean, std_dev=std_dev, read_length=read_length, sample_name=sample_name) + output.write(config_line) \ No newline at end of file |
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| diff -r 000000000000 -r f65530d07350 test-data/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/README Tue May 17 04:35:44 2016 -0400 |
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| @@ -0,0 +1,10 @@ +This is a collection of test data to be used with breakdancer. It consists of: + +an alignment file +a output bed file + +The details for the alignment file to be put into breakdancer are: +mean:227 +standard deviation:98 +read length:125 +sample:X_10000000_Hum1 |
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| diff -r 000000000000 -r f65530d07350 test-data/X_10000000_Hum1.bam |
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| Binary file test-data/X_10000000_Hum1.bam has changed |
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| diff -r 000000000000 -r f65530d07350 test-data/X_10000000_Hum1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/X_10000000_Hum1.bed Tue May 17 04:35:44 2016 -0400 |
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| b'@@ -0,0 +1,1144 @@\n+track name=X_131684_DEL_340\tdescription="BreakDancer X 131684 DEL 340"\tuseScore=0\n+chrX\t131994\t131868\tHWI-6298568|X_10000000_Hum1\t600\t1\t131994\t131868\t255,0,0\n+chrX\t131563\t131437\tHWI-6298568|X_10000000_Hum1\t600\t0\t131563\t131437\t0,0,255\n+chrX\t131994\t131868\tHWI-31657236|X_10000000_Hum1\t600\t1\t131994\t131868\t255,0,0\n+chrX\t131563\t131437\tHWI-31657236|X_10000000_Hum1\t600\t0\t131563\t131437\t0,0,255\n+chrX\t131994\t131868\tHWI-32617812|X_10000000_Hum1\t600\t1\t131994\t131868\t255,0,0\n+chrX\t131563\t131437\tHWI-32617812|X_10000000_Hum1\t600\t0\t131563\t131437\t0,0,255\n+chrX\t132015\t131910\tHWI-33492886|X_10000000_Hum1\t600\t1\t132015\t131910\t255,0,0\n+chrX\t131563\t131437\tHWI-33492886|X_10000000_Hum1\t600\t0\t131563\t131437\t0,0,255\n+chrX\t132018\t131892\tHWI-19903919|X_10000000_Hum1\t600\t1\t132018\t131892\t255,0,0\n+chrX\t131531\t131405\tHWI-19903919|X_10000000_Hum1\t600\t0\t131531\t131405\t0,0,255\n+track name=X_142444_ITX_-102\tdescription="BreakDancer X 142444 ITX -102"\tuseScore=0\n+chrX\t142487\t142374\tHWI-1310581|X_10000000_Hum1\t600\t0\t142487\t142374\t0,0,255\n+chrX\t142486\t142360\tHWI-1310581|X_10000000_Hum1\t600\t1\t142486\t142360\t255,0,0\n+chrX\t142487\t142361\tHWI-26162395|X_10000000_Hum1\t600\t0\t142487\t142361\t0,0,255\n+chrX\t142486\t142360\tHWI-26162395|X_10000000_Hum1\t600\t1\t142486\t142360\t255,0,0\n+chrX\t142487\t142361\tHWI-36006580|X_10000000_Hum1\t600\t0\t142487\t142361\t0,0,255\n+chrX\t142486\t142360\tHWI-36006580|X_10000000_Hum1\t600\t1\t142486\t142360\t255,0,0\n+chrX\t142487\t142361\tHWI-43085375|X_10000000_Hum1\t600\t0\t142487\t142361\t0,0,255\n+chrX\t142486\t142360\tHWI-43085375|X_10000000_Hum1\t600\t1\t142486\t142360\t255,0,0\n+track name=X_142690_ITX_-104\tdescription="BreakDancer X 142690 ITX -104"\tuseScore=0\n+chrX\t142691\t142565\tHWI-13343719|X_10000000_Hum1\t600\t0\t142691\t142565\t0,0,255\n+chrX\t142689\t142563\tHWI-13343719|X_10000000_Hum1\t600\t1\t142689\t142563\t255,0,0\n+chrX\t142691\t142565\tHWI-14372761|X_10000000_Hum1\t600\t0\t142691\t142565\t0,0,255\n+chrX\t142690\t142564\tHWI-14372761|X_10000000_Hum1\t600\t1\t142690\t142564\t255,0,0\n+track name=X_145921_DEL_526\tdescription="BreakDancer X 145921 DEL 526"\tuseScore=0\n+chrX\t146394\t146268\tHWI-10337428|X_10000000_Hum1\t600\t1\t146394\t146268\t255,0,0\n+chrX\t145766\t145640\tHWI-10337428|X_10000000_Hum1\t600\t0\t145766\t145640\t0,0,255\n+chrX\t146404\t146288\tHWI-10048340|X_10000000_Hum1\t600\t1\t146404\t146288\t255,0,0\n+chrX\t145766\t145674\tHWI-10048340|X_10000000_Hum1\t600\t0\t145766\t145674\t0,0,255\n+track name=X_151718_DEL_331\tdescription="BreakDancer X 151718 DEL 331"\tuseScore=0\n+chrX\t151997\t151871\tHWI-6298273|X_10000000_Hum1\t600\t1\t151997\t151871\t255,0,0\n+chrX\t151597\t151471\tHWI-6298273|X_10000000_Hum1\t600\t0\t151597\t151471\t0,0,255\n+chrX\t151997\t151871\tHWI-25827772|X_10000000_Hum1\t600\t1\t151997\t151871\t255,0,0\n+chrX\t151597\t151471\tHWI-25827772|X_10000000_Hum1\t600\t0\t151597\t151471\t0,0,255\n+chrX\t152019\t151893\tHWI-19776492|X_10000000_Hum1\t600\t1\t152019\t151893\t255,0,0\n+chrX\t151554\t151428\tHWI-19776492|X_10000000_Hum1\t600\t0\t151554\t151428\t0,0,255\n+chrX\t152019\t151893\tHWI-29820858|X_10000000_Hum1\t600\t1\t152019\t151893\t255,0,0\n+chrX\t151554\t151455\tHWI-29820858|X_10000000_Hum1\t600\t0\t151554\t151455\t0,0,255\n+track name=X_155647_ITX_-102\tdescription="BreakDancer X 155647 ITX -102"\tuseScore=0\n+chrX\t155647\t155596\tHWI-2147919|X_10000000_Hum1\t580\t0\t155647\t155596\t0,0,255\n+chrX\t155646\t155520\tHWI-2147919|X_10000000_Hum1\t600\t1\t155646\t155520\t255,0,0\n+chrX\t155647\t155521\tHWI-13386630|X_10000000_Hum1\t600\t0\t155647\t155521\t0,0,255\n+chrX\t155646\t155520\tHWI-13386630|X_10000000_Hum1\t600\t1\t155646\t155520\t255,0,0\n+chrX\t155647\t155521\tHWI-45221094|X_10000000_Hum1\t600\t0\t155647\t155521\t0,0,255\n+chrX\t155646\t155520\tHWI-45221094|X_10000000_Hum1\t600\t1\t155646\t155520\t255,0,0\n+track name=X_157963_DEL_432\tdescription="BreakDancer X 157963 DEL 432"\tuseScore=0\n+chrX\t158376\t158250\tHWI-5008667|X_10000000_Hum1\t600\t1\t158376\t158250\t255,0,0\n+chrX\t157842\t157716\tHWI-5008667|X_10000000_Hum1\t600\t0\t157842\t157716\t0,0,255\n+chrX\t158394\t158286\tHWI-34737497|X_10000000_Hum1\t600\t1\t158394\t158286\t255,0,0\n+chrX\t157842\t157716\tHWI-34737497|X_10000000_Hum1\t600\t0\t157842\t157716\t0,0,255\n+chrX\t158425\t15'..b'-29186998|X_10000000_Hum1\t600\t1\t922107\t921981\t255,0,0\n+chrX\t922108\t921982\tHWI-40125118|X_10000000_Hum1\t600\t0\t922108\t921982\t0,0,255\n+chrX\t922107\t921981\tHWI-40125118|X_10000000_Hum1\t600\t1\t922107\t921981\t255,0,0\n+track name=X_949787_ITX_-103\tdescription="BreakDancer X 949787 ITX -103"\tuseScore=0\n+chrX\t949788\t949662\tHWI-6045342|X_10000000_Hum1\t600\t0\t949788\t949662\t0,0,255\n+chrX\t949786\t949660\tHWI-6045342|X_10000000_Hum1\t600\t1\t949786\t949660\t255,0,0\n+chrX\t949788\t949662\tHWI-34809432|X_10000000_Hum1\t600\t0\t949788\t949662\t0,0,255\n+chrX\t949786\t949660\tHWI-34809432|X_10000000_Hum1\t600\t1\t949786\t949660\t255,0,0\n+track name=X_970591_DEL_319\tdescription="BreakDancer X 970591 DEL 319"\tuseScore=0\n+chrX\t970926\t970870\tHWI-2013544|X_10000000_Hum1\t600\t1\t970926\t970870\t255,0,0\n+chrX\t970442\t970316\tHWI-2013544|X_10000000_Hum1\t600\t0\t970442\t970316\t0,0,255\n+chrX\t970926\t970870\tHWI-8849818|X_10000000_Hum1\t600\t1\t970926\t970870\t255,0,0\n+chrX\t970442\t970316\tHWI-8849818|X_10000000_Hum1\t600\t0\t970442\t970316\t0,0,255\n+chrX\t970926\t970870\tHWI-18487959|X_10000000_Hum1\t600\t1\t970926\t970870\t255,0,0\n+chrX\t970442\t970316\tHWI-18487959|X_10000000_Hum1\t600\t0\t970442\t970316\t0,0,255\n+chrX\t970926\t970870\tHWI-25393900|X_10000000_Hum1\t600\t1\t970926\t970870\t255,0,0\n+chrX\t970442\t970321\tHWI-25393900|X_10000000_Hum1\t600\t0\t970442\t970321\t0,0,255\n+chrX\t970926\t970870\tHWI-38484889|X_10000000_Hum1\t600\t1\t970926\t970870\t255,0,0\n+chrX\t970442\t970316\tHWI-38484889|X_10000000_Hum1\t600\t0\t970442\t970316\t0,0,255\n+chrX\t970973\t970913\tHWI-253607|X_10000000_Hum1\t600\t1\t970973\t970913\t255,0,0\n+chrX\t970470\t970344\tHWI-253607|X_10000000_Hum1\t600\t0\t970470\t970344\t0,0,255\n+chrX\t970987\t970941\tHWI-17463305|X_10000000_Hum1\t600\t1\t970987\t970941\t255,0,0\n+chrX\t970470\t970344\tHWI-17463305|X_10000000_Hum1\t600\t0\t970470\t970344\t0,0,255\n+track name=X_971930_ITX_-102\tdescription="BreakDancer X 971930 ITX -102"\tuseScore=0\n+chrX\t971968\t971842\tHWI-902251|X_10000000_Hum1\t600\t0\t971968\t971842\t0,0,255\n+chrX\t971967\t971841\tHWI-902251|X_10000000_Hum1\t600\t1\t971967\t971841\t255,0,0\n+chrX\t971968\t971842\tHWI-1661657|X_10000000_Hum1\t600\t0\t971968\t971842\t0,0,255\n+chrX\t971967\t971841\tHWI-1661657|X_10000000_Hum1\t600\t1\t971967\t971841\t255,0,0\n+chrX\t971968\t971842\tHWI-33664636|X_10000000_Hum1\t600\t0\t971968\t971842\t0,0,255\n+chrX\t971967\t971841\tHWI-33664636|X_10000000_Hum1\t600\t1\t971967\t971841\t255,0,0\n+track name=X_976376_DEL_419\tdescription="BreakDancer X 976376 DEL 419"\tuseScore=0\n+chrX\t976722\t976596\tHWI-21613675|X_10000000_Hum1\t600\t1\t976722\t976596\t255,0,0\n+chrX\t976192\t976071\tHWI-21613675|X_10000000_Hum1\t600\t0\t976192\t976071\t0,0,255\n+chrX\t976722\t976596\tHWI-28875065|X_10000000_Hum1\t600\t1\t976722\t976596\t255,0,0\n+chrX\t976192\t976066\tHWI-28875065|X_10000000_Hum1\t600\t0\t976192\t976066\t0,0,255\n+chrX\t976722\t976596\tHWI-44872323|X_10000000_Hum1\t600\t1\t976722\t976596\t255,0,0\n+chrX\t976192\t976066\tHWI-44872323|X_10000000_Hum1\t600\t0\t976192\t976066\t0,0,255\n+chrX\t976745\t976619\tHWI-31479971|X_10000000_Hum1\t600\t1\t976745\t976619\t255,0,0\n+chrX\t976255\t976129\tHWI-31479971|X_10000000_Hum1\t600\t0\t976255\t976129\t0,0,255\n+chrX\t976745\t976619\tHWI-43689087|X_10000000_Hum1\t600\t1\t976745\t976619\t255,0,0\n+chrX\t976255\t976129\tHWI-43689087|X_10000000_Hum1\t600\t0\t976255\t976129\t0,0,255\n+chrX\t976773\t976647\tHWI-30122343|X_10000000_Hum1\t600\t1\t976773\t976647\t255,0,0\n+chrX\t976236\t976116\tHWI-30122343|X_10000000_Hum1\t600\t0\t976236\t976116\t0,0,255\n+chrX\t976773\t976647\tHWI-30933434|X_10000000_Hum1\t600\t1\t976773\t976647\t255,0,0\n+chrX\t976236\t976110\tHWI-30933434|X_10000000_Hum1\t600\t0\t976236\t976110\t0,0,255\n+track name=X_999900_ITX_-104\tdescription="BreakDancer X 999900 ITX -104"\tuseScore=0\n+chrX\t999913\t999787\tHWI-4720434|X_10000000_Hum1\t600\t0\t999913\t999787\t0,0,255\n+chrX\t999911\t999785\tHWI-4720434|X_10000000_Hum1\t600\t1\t999911\t999785\t255,0,0\n+chrX\t999913\t999787\tHWI-30372156|X_10000000_Hum1\t600\t0\t999913\t999787\t0,0,255\n+chrX\t999911\t999785\tHWI-30372156|X_10000000_Hum1\t600\t1\t999911\t999785\t255,0,0\n+chrX\t999913\t999787\tHWI-34394963|X_10000000_Hum1\t600\t0\t999913\t999787\t0,0,255\n+chrX\t999911\t999785\tHWI-34394963|X_10000000_Hum1\t600\t1\t999911\t999785\t255,0,0\n' |