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Old 07-13-2012, 01:42 PM   #1
tutenkhamun
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Default Breakdancer multiple files with the same library

Hi,

I was wondering if breakdancer_max supports multiple BAM files with the same library?

Thanks.
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Old 10-11-2012, 09:49 AM   #2
vinay052003
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If you are sure that all the bam files are from the same library i.e. same insert size, then you can just merge and coordinate sort your bam files and run the BreakDancer.
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Old 10-15-2012, 08:26 AM   #3
jflowers
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I have a related question. I have a merged bam with multiple samples, each from a single library. Can breakdancer be run on the merged bam?
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Old 10-15-2012, 09:46 AM   #4
cwhelan
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Yes, Breakdancer supports merged bam files from multiple libraries as long as the SAM header and records have all of the RG information for each library/read. I've had success using the bam2cfg script to prep such a BAM file for Breakdancer, and the Breakdancer output will show how many supporting reads for each SV call came from each library, if that's important to you.
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Old 10-22-2012, 11:00 AM   #5
jflowers
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Quote:
Originally Posted by cwhelan View Post
Yes, Breakdancer supports merged bam files from multiple libraries as long as the SAM header and records have all of the RG information for each library/read. I've had success using the bam2cfg script to prep such a BAM file for Breakdancer, and the Breakdancer output will show how many supporting reads for each SV call came from each library, if that's important to you.
Hi cwhelan,

I do want to see how many supporting reads for each SV call come from each library. However, the output I have generated using bam2cfg.pl followed by breakdancer_max on a merged bam don't yield a column for each library showing how many reads support the variant in that library.

In my case, libraries and readgroups are the same (one library was sequenced for each sample). The bam2cfg.pl appears to have recognized this as there is an entry in the cfg output for each readgroup.

Here is an example of the first 2 lines from the bam2cfg.pl output:
readgroup:CR2343-1 platform:Illumina map:bwa_msrsd_M.bam readlen:51.00 lib:CR2343-1 num:10001 lower:54.15 upper:668.01 mean:388.84 std:76.79 SWnormal
ity:-44.09 flag:1(0.06%)18(97.36%)2(0.25%)32(2.20%)4(0.05%)8(0.07%)20528 exe:samtools view
readgroup:CR1952-1 platform:Illumina map:bwa_msrsd_M.bam readlen:51.00 lib:CR1952-1 num:10001 lower:147.79 upper:589.19 mean:395.16 std:55.13 SWnormal
ity:-43.45 flag:1(0.03%)18(98.42%)2(0.04%)32(1.47%)4(0.02%)8(0.01%)20214 exe:samtools view

The breakdancer_max output shows the number of reads supporting the structural variant for the map file, not for each readgroup or library (in my case: bwa_msrsd_M.bam, as you can see from the bam2cfg output). Here is the relevant header line and a single entry:

#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib bwa_msrsd_M.bam
chromosome_1 15364 2237+1752- chromosome_1 154125 4379+4076- INS -231 99 214 bwa_msrsd_M.bam|214 1.80

Notice that the num_Reads_lib column has "bwa_msrsd_M.bam|214" which is the name of the map (bam) file not the library (which again, in my case is synonymous with sample).

When you run breakdancer_max on a merged bam, do you get a column of output for each library?

Jonathan
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Old 10-22-2012, 11:37 AM   #6
jflowers
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I think I found the answer to my problem. If you want breakdancer_max to report reads supporting a variant for each library, you apparently need to use the -a option.
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Old 10-23-2012, 08:38 AM   #7
cwhelan
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Yes, that's what I was going to suggest.
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Old 11-06-2012, 07:54 AM   #8
ralonso
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Hello,

I am calling breakdancer to see which structural variants are different from one sample to another. For these I do this two steps:
perl perl/bam2cfg.pl -g -h*ivia_040_10.bam*ivia_214_10.bam*> both.cfg
breakdancer_max *-g bed *both.cfg > both.sv

My problem is that breakdancer is not reporting well the sv, for example, I see the same sv in two different lines,line 2 and 3, in the file both.sv, it just changes two bases, and if you see it in IGV, is a perfect deletion in both samples*ex:

1. scaffold_1 348436 88+2- scaffold_1 349316 1+166- DEL 630 99 87 ivia_040_10.bam|84:ivia_214_10.bam|3 NA 0.30
2. scaffold_1 355952 122+0- scaffold_1 356266 1+247- DEL 329 99 122 ivia_040_10.bam|122 0.01 6.48
3. scaffold_1 355954 122+1- scaffold_1 356266 0+124- DEL 333 99 122 ivia_214_10.bam|122 NA NA
4. scaffold_1 360645 36+35- scaffold_1 361319 36+35- INS -200 99 35 ivia_040_10.bam|20:ivia_214_10.bam|15 NA NA

The thing is that some of them are well detected, like in line 1 or 4.

could anyone help me with this?

Thanks!
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Old 04-17-2015, 02:45 PM   #9
yjzhang913
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Quote:
Originally Posted by jflowers View Post
I think I found the answer to my problem. If you want breakdancer_max to report reads supporting a variant for each library, you apparently need to use the -a option.
Hi, I have use the -a options in breakdancer 1.4.5. but the results I obtain is like this:
what are "0.09 NA"? I don't believe they are the number of supported reads in each library.


#41.bam mean:327.2 std:110.45 uppercutoff:659.75 lowercutoff:100 readlen:97.03 library:41 reflen:273108516 seqcov:38.7174 phycov:65.2805 1:98928 2:709112 3:39620 4:236811 8:104415 32:510691
#44.bam mean:335.46 std:123.56 uppercutoff:716.37 lowercutoff:100 readlen:97.24 library:44 reflen:273108516 seqcov:0 phycov:0
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib 41.bam 44.bam
2L 13997 48+6- 2L 14849 3+24- DEL 859 99 24 41.bam|24 0.01 NA
2L 13997 48+6- 2L 15011 1+15- DEL 972 99 12 41.bam|12 0.09 NA
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