[megnetz]

Hello! I've been running breakdancer on 1000genomes data and it works fine except it generates a LOT of inserts that I suspect are false positives. This makes finding real insertions difficult. Increasing the number of needed pairs for calling a variant to for example 4 diminishes the noise but doesn't remove it. Anyone else having this problem?

Another thing, when running breakdancer on many BAM-files at once it generates completely different data compared to running them individually. For I example I find the same deletion in every single one of 20 individuals but when combining them in the bam2cfg script this deletion disappears.

Thank you for your time!

/Magnus

[hepcat72]

I am trying to run BreakDancer Max on a data set including only one library. Alignment with BWA created an alignment file in which no library name was specified (no @RG header). The bam2cfg.pl included in BreakDancer-0.0.1 (which seems to have incorporated the suggestion from pallo) ran and produced the following config file (config.file):

readgroup:NA platform:illumina map:../Poli/s_1_sequence.bam readlen:75.00 lib:NA num:10001 lower:130.99 upper:275.98 mean:210.78 std:18.14 exe:samtools view

We then ran BrakDancer Max with the following command

perl BreakDancerMax.pl config.file >output.file

and obtained the following (empty) output file
#../Poli/s_1_sequence.bam mean:210.780 std:18.140 uppercutoff:275.980 lowercutoff:130.990 readlen:75.000 library:NA reflen:484660925 seqcov:4.744x phycov:6.667x 1:1784 2:60640 3:59812 4:8280 8:2320 32:48156
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib Allele_frequency Version Run_Param

Can someone help with this issue?

I'm having the same problem. I get a cfg file that looks fine, but only the header comes out of BreakDancerMax. I know that the data should have SVs in it because it's from a published paper about SVs. How can one debug this issue?

[pickw]

Please try the c version from
svn co https://breakdancer.svn.sourceforge....ot/breakdancer breakdancer

The perl version is becoming obsolete.

[ramouz87]

Hi,
Did you sort and index your bam file ? If not, doing so may solve the problem
Best,
Ramzi

[hepcat72]

I sorted via MosaikSort which was then converted to bam. I'm running another attempt right now after a sort attempt with `samtools sort`. I'll try an index next if that doesn't work. Do I have to supply the index file or does BreakDancer look for the bai file extension automatically?

Thanks,
Rob

[hepcat72]

I sorted the file using `samtools sort`. I indexed it as well. Still no luck. My output files, aside from the headers, are empty. breakdancer_max complains about missing LB tags in the @RG header line (of which there's only 1). I supplied a file via -f telling bam2cfg.pl to use "NA" as the library for the only readgroup. I didn't indicate the bai file anywhere. Does it find it automatically?

[francesconea]

Hi All,

any news about this BreakDancer usage? In addiction, what about BreakDancer Mini? Is that already obsolete? I thought it was good to compare indels retrieval results...

[mei404]

breakdancer bam2cfg error

when i run perl /usr/local/src/breakdancer-1.1_2011_02_21/perl/bam2cfg.pl ./test_sort.bam , this two error,
Use of uninitialized value in hash element at /usr/local/src/breakdancer-1.1_2011_02_21/perl/bam2cfg.pl line 71, <BAM> line 26.
Use of uninitialized value in hash element at /usr/local/src/breakdancer-1.1_2011_02_21/perl/bam2cfg.pl line 173.
who know how to solve?
I feel anxious! thanks!

[hanifk]

I am trying to run BreakDancer Max on a data set including only one library. Alignment with BWA created an alignment file in which no library name was specified (no @RG header). The bam2cfg.pl included in BreakDancer-0.0.1 (which seems to have incorporated the suggestion from pallo) ran and produced the following config file (config.file):

readgroup:NA platform:illumina map:../Poli/s_1_sequence.bam readlen:75.00 lib:NA num:10001 lower:130.99 upper:275.98 mean:210.78 std:18.14 exe:samtools view

We then ran BrakDancer Max with the following command

perl BreakDancerMax.pl config.file >output.file

and obtained the following (empty) output file
#../Poli/s_1_sequence.bam mean:210.780 std:18.140 uppercutoff:275.980 lowercutoff:130.990 readlen:75.000 library:NA reflen:484660925 seqcov:4.744x phycov:6.667x 1:1784 2:60640 3:59812 4:8280 8:2320 32:48156
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib Allele_frequency Version Run_Param

Can someone help with this issue?

I have the same problem with you, did you solve that?

[ritzriya]

when i run perl /usr/local/src/breakdancer-1.1_2011_02_21/perl/bam2cfg.pl ./test_sort.bam , this two error,
Use of uninitialized value in hash element at /usr/local/src/breakdancer-1.1_2011_02_21/perl/bam2cfg.pl line 71, <BAM> line 26.
Use of uninitialized value in hash element at /usr/local/src/breakdancer-1.1_2011_02_21/perl/bam2cfg.pl line 173.
who know how to solve?
I feel anxious! thanks!

Dear mei404,

I am facing the same problem/error. Did you find any solution to this?

Thanks in advance.

[jwhite]

Hi,
Thanks for you reply, I've tried with BWA but still have an empty file when appliying bam2cfg.pl
bwa sampe -a 5000 ~/genomes/Homo_sapiens.GRCh37.56.dna.toplevel.fa ./sai/s_8_1_sequence.fq.bwa.align.sai ./sai/s_8_2_sequence_50b.fq.bwa.align.sai ./fastq/s_8_1_sequence.fq ./fastq/s_8_2_sequence_50b.fq > ./sam/pr_5000_2_50b.bwa.sam

bam2cfg.pl ./bam/pr_5000_2_50b.bwa.bam > ./sv/pr_5000_2_50b.bwa.bam.lst

Beside, I get no error message.

Any intuition regarding the origin of this issue.
Thanks in advance
Best,
Ramzi

Hello,

Do your BAM files include the read group Library (@RG LB:xyz) tag? BreakDancer seems to need the read group in order to work. I had to replace the headers in all my BAM files just to get this program to work. e.g.:

samtools view -H bamfile.bam > header.bam

Edit the header.bam and add the @RG line to include: @RG ID:xyz SM:xyz LB:xyz

Replace the header in your bam file:

samtools reheader header.bam bamfile.bam

Then use bam2cfg.pl. I had to do these one at a time, then run bam2cfg.pl with '>>' to capture output in a single file:

bam2cfg.pl -q 20 -f librarylist -g -h *.bam >> config

(The librarylist is probably not necessary; it could not compensate for BAM files with no LIBrary information. )

HTH,

Joe

[simobioinfo]

Hi,
I'm trying to analyze with breakdancer data coming from ion torrent, which were aligned through tmap.
I ran bam2cfg.pl but I obtained an empty file.
This is the message:
[Wed Sep 9 15:26:19 2015 ./bam2cfg.pl] Closing BAM file
[Wed Sep 9 15:26:19 2015 ./bam2cfg.pl] Send TERM signal for 4992
[Wed Sep 9 15:26:21 2015 ./bam2cfg.pl] samtools pid process 4992 is still there...
[Wed Sep 9 15:26:21 2015 ./bam2cfg.pl] invoking kill -9 on 4992 ...
[Wed Sep 9 15:26:21 2015 ./bam2cfg.pl] Closing samtools process : 4992

At the beginning I have error regarding RG group and so through picard AddOrReplaceReadGroup I modified it.
Now I don't know how to solve this issue.
What is the problem?
Could anybody help me?