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Hi,

As title, What is the meaning of positive and negative value of size of
intra-chromosome translocation?

Many thanks,
CR

Hi!

I'm facing problems to generate the cfgfile with bam2cfg option from breakdancer.

First I thought it was just the RG header that was wrong in my bam file, but now I already fixed it and still, it is not generating. Before it was creating an empty cfgfile, as I saw in other issues, but now it's not creating a cfg file at all.

Is this bam2cfg still working in the latest version? Because I don't see many pieces of information about it.

And when I launch the command, it finishes saying to me that the job was successfully completed (?)
Here follows my command line and my output file:

COMMAND:

#!/usr/bin/env
module add /breakdancer/1.4.5
bam2cfg.pl -g -h sample.sorted.bam > sample.cfg

OUTPUT:

SBD_KRB5CCNAME_VAL=
LSF_VERSION=27
LOGNAME=adibatti
LSB_UNIXGROUP_INT=cig_reym
LSB_BATCH_NEW_SESSION=y
HOSTTYPE=X86_64
LSB_BATCH_JID=992776
LSB_JOBRES_PID=25148
LSB_JOBID=992776
LSB_JOBINDEX=0
LSB_JOBFILENAME=/home/adibatti/.lsbatch/1534151815.992776
LSB_CHKFILENAME=/home/adibatti/.lsbatch/1534151815.992776
LSB_TRAPSIGS=trap # 15 10 12 2
LSB_HOSTS=cpt133 cpt133
LSB_MCPU_HOSTS=cpt133 2
LSB_QUEUE=normal
LSB_JOBNAME=cfgfile
LSFUSER=adibatti
USER=adibatti
LSB_JOB_EXECUSER=adibatti
LSB_EXIT_PRE_ABORT=99
LS_EXEC_T=START
BSUB_BLOCK_EXEC_HOST=
PATH=/bin:/usr/bin/:/usr/mbin:/local/bin:/usr/local:/usr/ucb
LS_JOBPID=25148
LS_SUBCWD=/scratch/cluster/monthly/adibatti/WGS
LSB_SUB_HOST=frt
LSB_SUB_USER=adibatti
LSB_SUB_RES_REQ= rusage[mem=1000] span[hosts=1]
LSB_MAX_NUM_PROCESSORS=2
LSB_EXEC_HOSTTYPE=X86_64
LSF_ENVDIR=/mnt/common/lsf/conf
LSF_EGO_ENVDIR=/mnt/common/lsf/conf/ego/prdclst/kernel
LSF_SERVERDIR=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/etc
LSF_BINDIR=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/bin
LSF_LOGDIR=/mnt/common/lsf/log
LSF_LIBDIR=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/lib
LD_LIBRARY_PATH=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/lib
LSB_JOBEXIT_STAT=0
LSB_EXEC_CLUSTER=prdclst
LSB_EEXEC_REAL_UID=
LSB_EEXEC_REAL_GID=
LSB_EFFECTIVE_RSRCREQ=select[ (((type == any)&&(tmp>1024)))] order[r1m:ut] rusage[mem=1000.00] span[hosts=1] same[model]
LSB_DJOB_NUMPROC=2
LSF_LIC_FEATURES_NEEDED=543682721
LSF_CGROUP_TOPDIR_KEY=prdclst
LSF_JOB_TIMESTAMP_VALUE=1534151816
PWD=/scratch/cluster/monthly/adibatti/WGS
HOME=/home/adibatti
LSF_JOB_TMPDIR=/tmp/992776.tmpdir
LSB_DJOB_HOSTFILE=/home/adibatti/.lsbatch/1534151815.992776.hostfile
SHELL=/bin/env

Thank you!?

Hello,

We are planning a genome sequencing project with the aim of detecting dna
translocations and inversions in mutated plants of Sorghum bicolor compared
to reference genome. For that purpose we are planning to use BreakDancer.

Prior to sequencing we would like to know what is the optimal sequencing
technique for the tool to work ?:

Insert length (including or not including the pair of reads)? Average
genome coverage? Reads sequence length? And any other technical
considerations that we should be concerned about in order to learn about
genomic aberrations.

Many thanks in advance

Inbar

------------------

*Inbar Plaschkes*

Bioinformatician

Faculty of Agriculture, Food and Environment

The Hebrew University of Jerusalem

Rehovot, Israel, 7610010

phone: 972-(0)89489498 <08-948-9498>

cell: 972-(0)547-915931

e-mail: in...@ma...

Hi Breakdancer team,

I am attempting to use Breakdancer and I am running into some issues trying
to get the initial configuration file using the command: perl bam2cfg.pl -g
-h *BAM_files* > config_file. I believe that my BAM file is not formatted
correctly for Breakdancer to recognize.

I have tried to use Samtools to reformat it but have not been successful. I
know it is important to have readgroup (@RG) tag in both the header and
each alignment in the BAM files. The samtools documentations has proved
rather unhelpful in helping me to accomplish this. What would you
recommend to ensure that my BAM file is formatted correctly so when it is
read it will produce a valid configuration file? Is there some sort of
existing pipeline to accomplish this?

Thank you so much for your help!

-- 

Best,

Chandler L. Petersen | Undergraduate Student Intern
Children's Cancer Therapy Development Institute
direct: (503) 781-4292 |  cha...@cc...  |  http://cc-TDI.org

Hi

I'm using Breakdancer to find a known deletion. Around half of my samples should have it, the others not.

-        I added library info: Unknown (using 'samtools view -H BAMFILE | sed 's/PL:ILLUMINA/PL:ILLUMINA\tLB:Unknown/'| samtools reheader - BAMFILE > REHEADER.bam)

-        I run bam2cfg (no errors)

-        I get multiple lines per individual (Each individual has one BAM file)

-        Then I run Breakdancer
The errors I get are:
[bam_rg2lib_put] duplicated @RG ID: C3P9AACXX_AUMEPM000000000005_CGATGT_L004_R1-trimmed\tPL:ILLUMINA
[bam_rg2lib_put] duplicated @RG ID: C4MLGACXX_AUMEPM000000000005_NoIndex_L002_RX-singleton\tPL:ILLUMINA
[bam_rg2lib_put] duplicated @RG ID: C4MLGACXX_AUMEPM000000000005_NoIndex_L002_RX-singleton\tPL:ILLUMINA
[bam_rg2lib_put] duplicated @RG ID: C4MLGACXX_AUMEPM000000000005_NoIndex_L002_RX-singleton\tPL:ILLUMINA
[bam_rg2lib_put] duplicated @RG ID: C3P9AACXX_AUMEPM000000000005_CGATGT_L005_R1-trimmed\tPL:ILLUMINA

The output also includes the deletion where I expect it, but also many more deletions and other SVs (I expect maybe less)
The output from Breakdancer looks normal, but error messages are normally not to be ignored. All my samples have this issue.
Any ideas if I need to worry and how to resolve it

Many thanks
Naomi

Ps not familiar with the headers in BAM files...

Perhaps helpful to try the version 1.1.2 at
https://sourceforge.net/projects/breakdancer/?source=directory <https://sourceforge.net/projects/breakdancer/?source=directory>
It actually had more updates.

> On Oct 19, 2016, at 1:40 AM, Joanna Giemza <joa...@un...> wrote:
> 
> Hi,
> 
> Breakdancer is not interpreting my config file well. I have a version 
> from github downloaded less than two months ago.
> 
> If my config file is:
> 
> map:/ccc/genostore/cont007/fg0034/fg0034/analyse/projet_FRENCHWGPREGO_474/ANALYSE/ANALYSE_F474_B00GWEI_HK27FCCXX_7_hs37d5/MAPPING_B00GWEI/reliable.realign/F474_DA_B00GWEI_HK27FCCXX_hs37d5_MERGE_PE_7.reliable.realign.bam 
> mean:376    std:85  readlen:150.00  exe:samtools view sample:B00GWEI
> 
> I have a message: open: No such file or directory
> ERROR: Failed to open samfile 
> /ccc/genostore/cont007/fg0034/fg0034/analyse/projet_FRENCHWGPREGO_474/ANALYSE/ANALYSE_F474_B00GWEI_HK27FCCXX_7_hs37d5/MAPPING_B00GWEI/reliable.realign/F474_DA_B00GWEI_HK27FCCXX_hs37d5_MERGE_PE_7.reliable.realign.bam 
> mean:376 std:85 readlen:150.00 exe:samtools view sample:B00GWEI
> 
> So I guess it thinks that the whole line of my config file is a path, 
> not just the value of map
> 
> If I change the order of keys, so that map is the last, I get:
> 
> ERROR: Required field 'map' not found in config at line 1!
> 
> I would be grateful if you could answer and suggest something. Thank you,
> Joanna
> 
> ------------------------------------------------------------------------------
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Hi,

Breakdancer is not interpreting my config file well. I have a version 
from github downloaded less than two months ago.

If my config file is:

map:/ccc/genostore/cont007/fg0034/fg0034/analyse/projet_FRENCHWGPREGO_474/ANALYSE/ANALYSE_F474_B00GWEI_HK27FCCXX_7_hs37d5/MAPPING_B00GWEI/reliable.realign/F474_DA_B00GWEI_HK27FCCXX_hs37d5_MERGE_PE_7.reliable.realign.bam 
mean:376    std:85  readlen:150.00  exe:samtools view sample:B00GWEI

I have a message: open: No such file or directory
ERROR: Failed to open samfile 
/ccc/genostore/cont007/fg0034/fg0034/analyse/projet_FRENCHWGPREGO_474/ANALYSE/ANALYSE_F474_B00GWEI_HK27FCCXX_7_hs37d5/MAPPING_B00GWEI/reliable.realign/F474_DA_B00GWEI_HK27FCCXX_hs37d5_MERGE_PE_7.reliable.realign.bam 
mean:376 std:85 readlen:150.00 exe:samtools view sample:B00GWEI

So I guess it thinks that the whole line of my config file is a path, 
not just the value of map

If I change the order of keys, so that map is the last, I get:

ERROR: Required field 'map' not found in config at line 1!

I would be grateful if you could answer and suggest something. Thank you,
Joanna

Does breakdancer use?

> On Oct 12, 2016, at 12:03 PM, Ken Chen <kch...@gm...> wrote:
> 
> Yes.  That would be a major change.
> 
>> On Oct 12, 2016, at 11:45 AM, Gmail <mk...@gm...> wrote:
>> 
>> Does/can the algorithm for CNVs incorporate barcoded reads?  (barcodes added pre pcr to help ID CNVs).  Am I right to think that this would be a major change in the analysis?
>> 
>> Mike
>> 
>> ------------------------------------------------------------------------------
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>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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> 

Yes.  That would be a major change.

> On Oct 12, 2016, at 11:45 AM, Gmail <mk...@gm...> wrote:
> 
> Does/can the algorithm for CNVs incorporate barcoded reads?  (barcodes added pre pcr to help ID CNVs).  Am I right to think that this would be a major change in the analysis?
> 
> Mike
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most 
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
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> Bre...@li...
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Does/can the algorithm for CNVs incorporate barcoded reads?  (barcodes added pre pcr to help ID CNVs).  Am I right to think that this would be a major change in the analysis?

Mike

Dear There,
Thanks for developing such a useful tool.

I made a config file with only one normal.bam file and run the
BreakDancer_max.pl, it return SOMETHING that i dont understand. Does it
mean SV in "normal" sample (it reported around 8000 SV !!! ).

Thanks
-- 
जितेन्द्र नारायण
Jitendra Narayan <http://bioinformaticsonline.com/profile/admin>
http://bioinformaticsonline.com/

Hi,

I downloaded BreakDancer from github. I've run it with the attached 
config file. Unfortunately I got error:

Error: no bams files in config file!

I am sure my paths are correct.

Thanks in advance for your help.

Regards,

Joanna Giemza

Hi, Recently I used the newest version of BD (v1.3.6). To my surprise, the output is the number of reads for all libraries in combined, not the number of reads for individual library. Is there any way to split? thanks, wenge

Hi,
We are using breakdancer-max to identifies SVs in a set of samples. We have noticed that in most cases the reported SVLEN for deletions (and other SV types) is very different from ENDPOS - POS. The explanation in the paper is very confusing:"The start and the end coordinates are defined as the inner boundaries of the constituent regions that are closest to the suspected breakpoints, and the size is estimated by subtracting the mean insert size from the average spanning distance in each library and then averaging across libraries."
Can you please elaborate on how you calculate SVLEN and identify the endpoints? 
Thank you!
Hi,

I am new to using BreakDancer. I am trying to run breakdancer_max (version 1.4.5, perl) with three BAM files, and the documentation says, "This step normally takes 12 hours or so for three bam files, 8 hours or so for two bam files for cpp version, around three days for perl version." However, when I run breakdancer_max, the script only takes about 20-30 minutes, and it doesn't appear to throw any errors. The output .ctx file is not empty, but it does not contain the expected translocation.

Is there a reason why the script is running so much more quickly than expecting (and still producing output)?

Thanks.

Hello,

I am new to breakdancer and have a simple question regarding output. Here is some sample output I received:

Sample_genome 116981 1067+1060- Sample_genome 117042 1067+1060- ITX -231 36 690 Sample_genome_coordinates-sort.bam|690 NA
Sample_genome 117042 1067+1060- Sample_genome 117066 358+322- INS -230 99 272 Sample_genome_coordinates-sort.bam|272 0.03
Sample_genome 123113 9864+736- Sample_genome 137482 465+60- INV 14633 99 231 Sample_genome_coordinates-sort.bam|231 1.77

My problem is determining the exact genomic coordinates specified for each variant. For example, the intra-chromosomal inversion is noted as beginning at position 116981 and ending at 117042. However, the length string indicates the variant is a total of “-231” bases long. I’m having trouble understanding what is actually going on in the genome. If there is a translocation occurring, I want to know the start and end coordinates of the origin site and the start and end coordinates of the insertion site. 

Similarly for inversions, if the start coordinate is 123113 and the end coordinate is 137842, should I just assume that this whole section is a possible inversion event using those start and end coordinates?

And for insertions, should I assume that the start coordinate (117042) is where the length of the variant (-230, so I guess an insertion size of 230 bases?) would be inserted?

Thanks for the assistance.
-Jacob

If you are working on a population of germline genomes, GenomeSTRiP may be an excellent choice for genotyping.
If you only have a single or a pair of genomes, you may want to try BreakDown for genotyping.
https://bcbweb.mdanderson.edu/main/BreakDown

On Dec 4, 2014, at 2:21 PM, "Chen, Peng (NIH/NIDDK) [F]" <pen...@ni...> wrote:

>  
> Hi there,
>  
> I am looking at the breakdancer  and pindel output files. I would like to get the genotypes for each individual and compare the results from the two software. I have googled but found no software for this purpose. An R package intansv do have the ability to merge files, but can’t extract quality scores and individual genotypes from the output files. Those may require reading the reference genome to get the exact alleles.
>  
> I am wondering if somebody have done the job and have a handy tool in hand that I can borrow or I must start scripting.
>  
> By the way, I am running BreakDancerMax-1.1.2. The output file lacks the last column which I suspect to be NA, in several lines. I am not sure if this is a software bug.
>  
> Best,
> Peng
>  
> ------------------------------------------------------------------------------
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Hi there,

I am looking at the breakdancer  and pindel output files. I would like to get the genotypes for each individual and compare the results from the two software. I have googled but found no software for this purpose. An R package intansv do have the ability to merge files, but can't extract quality scores and individual genotypes from the output files. Those may require reading the reference genome to get the exact alleles.

I am wondering if somebody have done the job and have a handy tool in hand that I can borrow or I must start scripting.

By the way, I am running BreakDancerMax-1.1.2. The output file lacks the last column which I suspect to be NA, in several lines. I am not sure if this is a software bug.

Best,
Peng

Hi,
    I have started using Breakdancer-1.1.2 to find deletions and inversions in a population. I used all bam files of this population to generate the cfg file. The options I used are "breakdancer-max -r 4 -c 4 -q 35". However the program has been running for more than 1000 hours. So I'd like to use the -o option to do Breakdancer analysis on chromosome to accelerate my analysis. But when I add -o to my options, a fault "Segmentation fault (core dumped)" came out. Now I question is how to use -o option and fix my problem?

Thanks so much your help

Eagerly waiting for your reply

Best Wishes

Joyce

I would analyze these libraries individually (provided each having sufficient coverage) and look for inversion breakpoints that are consistently detected.
Longer insert size would be more helpful to detect inversion breakpoints in repeats.
You would also try Delly.

On Nov 19, 2014, at 7:56 AM, Pallavi Chauhan <pal...@bi...> wrote:

> 
> From: Pallavi Chauhan
> Sent: Wednesday, November 19, 2014 2:55 PM
> To: he...@li...
> Cc: kc...@wu...
> Subject: Help with breakdancer
> 
> Hi,
> My name is Pallavi and i am working as a post doc at Lund University Lund Sweden.
> I have started using Breakdancer to find inversions in the assembled genome. I have certain queries regarding running Breakdancer. Before i state my queries i would like to give a brief introduction about my work.
> I have assembled a genome using illumina paired -end 170bp, 500bp, 2000bp and 5000bp insert size libraries. Now i want to find inversion within the genome, since we don't have any closely related reference genome, i was thinking to map the libraries against the assembled genome to find the inversions.
> Now my queries are-
> 
> 1) Whether mapping the libraries back to the assembled genome would give correct information about the inversions?.
> 2) Which library among four would you think can help to find the accurate inversions?
> 3) Can to suggest some other equally good tools to validate the inversion results?.
> 
> 
> Eagerly waiting for your reply
> Thanking you
> 
> Best Regards
> 
> 
> Pallavi
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
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> Bre...@li...
> https://lists.sourceforge.net/lists/listinfo/breakdancer-help

________________________________
From: Pallavi Chauhan
Sent: Wednesday, November 19, 2014 2:55 PM
To: he...@li...
Cc: kc...@wu...
Subject: Help with breakdancer

Hi,
My name is Pallavi and i am working as a post doc at Lund University Lund Sweden.
I have started using Breakdancer to find inversions in the assembled genome. I have certain queries regarding running Breakdancer. Before i state my queries i would like to give a brief introduction about my work.
I have assembled a genome using illumina paired -end 170bp, 500bp, 2000bp and 5000bp insert size libraries. Now i want to find inversion within the genome, since we don't have any closely related reference genome, i was thinking to map the libraries against the assembled genome to find the inversions.
Now my queries are-

1) Whether mapping the libraries back to the assembled genome would give correct information about the inversions?.
2) Which library among four would you think can help to find the accurate inversions?
3) Can to suggest some other equally good tools to validate the inversion results?.

Eagerly waiting for your reply
Thanking you

Best Regards

Pallavi

I am having a strange problem.
I am finding SV with breakdancer with several samples(lib)  and -d option
to save the reads that support SVs by lib.
But I  notice that the supporting reads file/s contain some other reads
than from that sample. Why is this so ? is it a bug ?

I wanted to take those reads and check in the bam file of where they are
but I could not! and found this problem.
any suggestions ? pls.

Regards,
Krishna

try increasing the -n to  1000000

Regards,
Krishna

On Wed, Aug 20, 2014 at 9:29 AM, hila sberro <hs...@gm...> wrote:

> Hi,
>
> I have a sam file which was generated using Novoalign. I am aligning
> microbiome data (paired end reads) against a set of microbial reference
> genomes.
> Many of the reads do not map or poorly map.
>
> When I run bam2cfg.pl on my bam file (either sorted or not) I get an
> empty cfg file with no error messages.
>
> I was wondering whether you could help me overcome this. I tried running
> with several different parameters (-g -h, -q 20, -n 1000) but nothing
> changed the result.
>
> Thanks in advance,
> Hila
>
>
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>
>

Hi,

I have a sam file which was generated using Novoalign. I am aligning
microbiome data (paired end reads) against a set of microbial reference
genomes.
Many of the reads do not map or poorly map.

When I run bam2cfg.pl on my bam file (either sorted or not) I get an empty
cfg file with no error messages.

I was wondering whether you could help me overcome this. I tried running
with several different parameters (-g -h, -q 20, -n 1000) but nothing
changed the result.

Thanks in advance,
Hila

Hi,

I have a result file (TUMOR.breakD.res.ctx) with BreakDancer. I want to plot
Circos using BreakDancer output. How do I should process BreakDancer output?

Thanks,

Qi Pan

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