Breakdancer output file question

[cmonat]

I think its the number of reads supporting the SV on each strand.

https://github.com/kenchen/breakdancer

Hi,

as I have read on the documentation you posted, the output should be constituted with 14 columns. But in my case, I have 17 !
I think that I have :
1. Chromosome 1
2. Position 1
3. Orientation 1
4. Chromosome 2
5. Position 2
6. Orientation 2
7. Type of a SV
8. Size of a SV
9. Confidence Score
10. Total number of supporting read pairs
11. Total number of supporting read pairs from each map file

But starting from here I'm not so sure
12. Estimated allele frequency

And this following I don't have:
13. Software version
14. The run parameters

My lines look like this:

#Chr1   Pos1    Orientation1    Chr2    Pos2    Orientation2    Type    Size    Score   num_Reads       num_Reads_lib   Sample_Barke_reheadered.bam     Sample_Bowman_reheadered.bam    Sample_Bulbosum_reheadered.bam  Sample_FT11_reheadered.bam      Sample_Igri_reheadered.bam      Sample_Pubiflorum_reheadered.bam
chr1H_part1     13958   241+168-        chr1H_part1     14031   241+168-        ITX     -212    34      3       ../barleyBAMs/Sample_Barke_reheadered.bam|3     NA      NA      NA      NA      NA      NA
chr1H_part1     22659   14+28-  chr1H_part1     22826   14+28-  ITX     -147    89      6       ../barleyBAMs/Sample_Bulbosum_reheadered.bam|6  NA      NA      NA      NA      NA      NA
chr1H_part1     51554   3+2-    chr1H_part1     51654   3+2-    ITX     -157    38      2       ../barleyBAMs/Sample_Pubiflorum_reheadered.bam|2        NA      NA      NA      NA      NA      NA
chr1H_part1     87327   42+24-  chr1H_part1     87429   42+24-  ITX     -179    99      18      ../barleyBAMs/Sample_Barke_reheadered.bam|5:../barleyBAMs/Sample_Bulbosum_reheadered.bam|12:../barleyBAMs/Sample_Pubiflorum_reheadered.bam|1    NA      NA      NA      NA      NA      NA
chr1H_part1     89261   11+5-   chr1H_part1     89314   11+5-   ITX     -176    74      4       ../barleyBAMs/Sample_Bulbosum_reheadered.bam|4  NA      NA      NA      NA      NA      NA
chr1H_part1     94809   25+24-  chr1H_part1     94860   25+24-  ITX     -154    99      15      ../barleyBAMs/Sample_Bulbosum_reheadered.bam|14:../barleyBAMs/Sample_Pubiflorum_reheadered.bam|1        NA      NA      NA      NA      NA      NA
chr1H_part1     95422   4+4-    chr1H_part1     95467   4+4-    ITX     -169    55      3       ../barleyBAMs/Sample_Bulbosum_reheadered.bam|3  NA      NA      NA      NA      NA      NA
chr1H_part1     97915   153+134-        chr1H_part1     98001   153+134-        ITX     -170    99      32      ../barleyBAMs/Sample_Barke_reheadered.bam|10:../barleyBAMs/Sample_Bulbosum_reheadered.bam|15:../barleyBAMs/Sample_Pubiflorum_reheadered.bam|7   NA      NA      NA      NA      NA      NA
chr1H_part1     99599   14+8-   chr1H_part1     99668   14+8-   ITX     -154    41      2       ../barleyBAMs/Sample_Pubiflorum_reheadered.bam|2        NA      NA      NA      NA      NA      NA
chr1H_part1     100374  7+3-    chr1H_part1     100449  7+3-    ITX     -164    39      3       ../barleyBAMs/Sample_Barke_reheadered.bam|1:../barleyBAMs/Sample_Bulbosum_reheadered.bam|2      NA      NA      NA      NA      NA      NA
chr1H_part1     124801  45+81-  chr1H_part1     133975  25+2-   ITX     8473    99      17      ../barleyBAMs/Sample_Barke_reheadered.bam|11:../barleyBAMs/Sample_Igri_reheadered.bam|6 0.21    0.00    0.03    0.09    0.25    0.02
chr1H_part1     124801  45+64-  chr1H_part1     134111  6+2-    ITX     5569    45      6       ../barleyBAMs/Sample_Barke_reheadered.bam|3:../barleyBAMs/Sample_Bulbosum_reheadered.bam|2:../barleyBAMs/Sample_Igri_reheadered.bam|1   0.21    0.00    0.03    0.10    0.25    0.02
chr1H_part1     125588  18+2-   chr1H_part1     126418  1+15-   DEL     890     45      8       ../barleyBAMs/Sample_Barke_reheadered.bam|5:../barleyBAMs/Sample_Igri_reheadered.bam|3  0.21    0.02    0.21    0.06    0.38    0.05
chr1H_part1     127470  8+33-   chr1H_part1     133703  9+33-   INV     5823    99      22      ../barleyBAMs/Sample_Barke_reheadered.bam|16:../barleyBAMs/Sample_Igri_reheadered.bam|6 0.16    0.00    0.01    0.06    0.18    0.00

Do you have an idea what are the final column I have? Is it the estimated allele frequency for each of my sample?

Thank you very much, have a nice day
C.

[ernfrid]

Vivek is right. For each coordinate that BreakDancer reports in that output line, the strand of every abnormal read at that location is reported. Thus, in your example, the region around the first coordiante had 11570 abnormally mapped reads on the forward strand and 11437 on the reverse. Note that this is way more than the number of reads reported as supporting the SV call. This is likely not a good call.

[vivek_]

Hi all,

I am using breakdancer to identify SVs on some whole genome samples. This is the first time that I am using the program and am a little confused on the output. The documentation hasn't been that helpful to me either.

Here is a line of the output:

22 28948681 11570+11437- 22 32903818 150360+152913- ITX 2117 5 2 WholeGenome_MatePair|2 0.00 BreakDancerMax-1.0r112 |o22

What I am confused about is columns 3 and 6 (bolded). I can't quite figure out what it is actually telling me.


Thanks for any clarification

I think its the number of reads supporting the SV on each strand.

https://github.com/kenchen/breakdancer

[lre1234]

Hi all,

I am using breakdancer to identify SVs on some whole genome samples. This is the first time that I am using the program and am a little confused on the output. The documentation hasn't been that helpful to me either.

Here is a line of the output:

22 28948681 11570+11437- 22 32903818 150360+152913- ITX 2117 5 2 WholeGenome_MatePair|2 0.00 BreakDancerMax-1.0r112 |o22

What I am confused about is columns 3 and 6 (bolded). I can't quite figure out what it is actually telling me.


Thanks for any clarification