Breakdancer -Q Flag Doesn'T Work

Question

[madkitty]

for some reason I just found out that whatever value enter after -q flag in breakdancer returns an empty file. Did anyone ever experienced that before ?

bam2cfg.pl -h sample1-1.bam sample1-2.bam > sample1-method2.cfg
breakdancer_max -q 60 sample1-method2.cfg > 1-MQ60.txt  >> returns an empty file
breakdancer_max -q 59 sample1-method2.cfg > 1-MQ59.txt  >> returns an empty file
breakdancer_max -q 45 sample1-method2.cfg > 1-MQ40.txt >> returns an empty file

If I run the same sample with the same cfg file but with no "-q" whatsoever, it returns an file with CNV called.

Answer 1

[Sukhi Singh]

May be I am wrong, but from the manual it say

The -q specifies the MAQ mapping quality threshold and can be used to skip reads that are not confidently mapped.

So, with this high score, none of the reads are passing the threshold, try lowering it and check again.

[madkitty]

I did lowered it to the default value 35 and it worked well, but we do have reads with a MAPQ of 60, when I select these reads with AWK and then run Breakdancer on it, it does work.. so that's why I don't understand why -q doesn't return the same result as my manual selection with AWK. Your nickname is from the Russell Peters show isn't it ? Are you from Toronto ?

[Sukhi Singh]

May be the encoding is different like Illumina (previous one) vs Sanger, check the mappers manual. Also, Its not my nick name, its my full real name which means (Light(deep) of happiness(Sukh)), nothing to do with the standup's (just because he moulded the it there). I am from India hope it clears something Cheers

[madkitty]

no offense intended. Thanks for your help!