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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
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Interpret the output bedpe file #54

Closed blsfoxfox closed 9 years ago

blsfoxfox commented 9 years ago

Hi Ryan,

I am working with catfish genome and just got the bedpe file from lumpy. However, some lines are bothering me. Could you please help me to interpret the result?

Following are part of the bedpe:

X 3093873 3093897 X 15991008 15991032 3825 6.55015e-06 + + TYPE:INVERSION IDS:2,6 STRANDS:++,6 MAX:X:3093886;X:15991021 95:X:3093885-3093887;X:15991020-15991022 X 1759864 1759888 X 15991631 15991655 3826 6.55015e-06 + - TYPE:DELETION IDS:2,6 STRANDS:+-,6 MAX:X:1759877;X:15991644 95:X:1759876-1759878;X:15991643-15991645 X 14485949 14485986 X 15991702 15991739 3827 0.000127914 - + TYPE:DUPLICATION IDS:2,4 STRANDS:-+,4 MAX:X:14485969;X:15991722 95:X:14485968-14485970;X:15991721-15991723 X 3093665 3093689 X 15991660 15991684 3828 6.55015e-06 - - TYPE:INVERSION IDS:2,6 STRANDS:--,6 MAX:X:3093678;X:15991673 95:X:3093677-3093679;X:15991672-15991674 X 15727549 15727586 X 15993001 15993038 3829 0.000127914 + + TYPE:INVERSION IDS:2,4 STRANDS:++,4 MAX:X:15727569;X:15993021 95:X:15727568-15727570;X:15993020-15993022 X 14185222 14185259 X 15993065 15993102 3830 0.000127914 + + TYPE:INVERSION IDS:2,4 STRANDS:++,4 MAX:X:14185242;X:15993085 95:X:14185241-14185243;X:15993084-15993086 X 15993899 15993924 X 15993950 15993987 3831 0.000144119 + + TYPE:INVERSION IDS:2,4 STRANDS:++,4 MAX:X:15993912;X:15993970 95:X:15993911-15993913;X:15993969-15993971

Does the first line mean there is a 12Mb inversion on Chromosome X between 3093873 and 15991032? If it is not ture, what can cause this? Mis-scaffolding? You can see there are many inversions with similar right breakpoints at 15.9 Mb, but different left breakpoints. Could this be erroneous or common?

Thanks,

Bob

ryanlayer commented 9 years ago

Sorry this took me so long to get back to you on this.

What is the coverage of your sample, and what was the command you ran?

blsfoxfox commented 9 years ago

The coverage is 100X, and the command was lumpy -mw 4 -tt 0.0 -pe bam_file:yype_abab_coco13_xxchromosome.discordant.pe.sort.bam,histo_file:yype_abab_coco13_xxchromosome.pe.histo,mean:7.12119085806,stdev:212.347788422,read_length:100,min_non_overlap:150,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:20 -sr bam_file:yype_abab_coco13_xxchromosome.sr.sort.bam,back_distance:20,weight:1,id:2,min_mapping_threshold:20 > yype_abab_coco13_chromosome.pesr.bedpe

The mean and stdev seems wrong to me, but it was generated by the pairend_distro.py script.

ryanlayer commented 9 years ago

Yes, the mean has got to be wrong.

Can you send me the first 100,000 lines of your bam file and your histo file (ryan.layer AT gmail)

On Thu, Mar 19, 2015 at 11:20 AM, blsfoxfox notifications@github.com wrote:

The coverage is 100X, and the command was lumpy -mw 4 -tt 0.0 -pe bam_file:yype_abab_coco13_xxchromosome.discordant.pe.sort.bam,histo_file:yype_abab_coco13_xxchromosome.pe.histo,mean:7.12119085806,stdev:212.347788422,read_length:100,min_non_overlap:150,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:20 -sr bam_file:yype_abab_coco13_xxchromosome.sr.sort.bam,back_distance:20,weight:1,id:2,min_mapping_threshold:20

yype_abab_coco13_chromosome.pesr.bedpe

The mean and stdev seems wrong to me, but it was generated by the pairend_distro.py script.

— Reply to this email directly or view it on GitHub https://github.com/arq5x/lumpy-sv/issues/54#issuecomment-83626243.

Ryan Layer