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Hi All,
I've been working with break dancer Max (perl version) for over two weeks now. Basically, I sequenced mate pair libraries (2-5 Kb) & aligned the reads to human ref seq using BWA aligner and then converted them in to bam files (sorted) using sam tools and further used breakdancer- bam2cfg.pl script. I've generated a config file and edited accordingly as below.The reason I edited the lower and upper value in the config file is because my goal is to detect SV > 2.5 Kb
Config file:
readgroup:NA platform:illumina map:/mml1/rakesh/bwadata/lanesixsampecommand/s_6_1_6_2_sequencesorted.bam.bam readlen:36.00 lib:NA num:9606 lower:200.00 upper:2200 mean:252.63 std:111.65 SWnormality:-39.92 exe:samtools view
Then, I imported the above config file in to Break_dancer_Max to detect SV greater than 2.5 Kb. When I see my Break dancer max output, I get lots of false positives with many deletions, Inversions, translocations but not many insertions >2.5 Kb.
Could someone suggest me, if I need to edit my config file to reduce my false positives? if yes, what values would you suggest to plugin in the lower, upper, mean and std options in my config file?
I’m kind of trying to get results with low false positives but just cannot. I feel I’m doing something wrong in my config file, because I either don’t entirely understand the config file options or the break dancer max script
I’m looking forward hearing from you all
Thank you very much
I've been working with break dancer Max (perl version) for over two weeks now. Basically, I sequenced mate pair libraries (2-5 Kb) & aligned the reads to human ref seq using BWA aligner and then converted them in to bam files (sorted) using sam tools and further used breakdancer- bam2cfg.pl script. I've generated a config file and edited accordingly as below.The reason I edited the lower and upper value in the config file is because my goal is to detect SV > 2.5 Kb
Config file:
readgroup:NA platform:illumina map:/mml1/rakesh/bwadata/lanesixsampecommand/s_6_1_6_2_sequencesorted.bam.bam readlen:36.00 lib:NA num:9606 lower:200.00 upper:2200 mean:252.63 std:111.65 SWnormality:-39.92 exe:samtools view
Then, I imported the above config file in to Break_dancer_Max to detect SV greater than 2.5 Kb. When I see my Break dancer max output, I get lots of false positives with many deletions, Inversions, translocations but not many insertions >2.5 Kb.
Could someone suggest me, if I need to edit my config file to reduce my false positives? if yes, what values would you suggest to plugin in the lower, upper, mean and std options in my config file?
I’m kind of trying to get results with low false positives but just cannot. I feel I’m doing something wrong in my config file, because I either don’t entirely understand the config file options or the break dancer max script
I’m looking forward hearing from you all
Thank you very much