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Old 10-04-2013, 04:20 AM   #7
Pengfei Liu
Location: Beijing

Join Date: Nov 2012
Posts: 16

Originally Posted by blubucki View Post
Hello everyone, this is my 1st post on this great forum and I look forward to your help.
I am trying to find the chimeric/fusion/split reads in my WGS NGS library. I tried bwasw with SE reads or PE alignment,.but not sure how it flags the chimeric/split reads in the output sam file. Or if there's another way to find them.
Can someone please help me in this.
Thanks a lot.
Sorry, I use bwa-mem to do alignment. I have tested, in that, -a , -M will affect the output. -a will produce all alignment (so, secondary alignment with 0x100 will appear), and chimeric alignment will with 0x800. but if you use both -a and -M, chimeric alignment and secondary alignment will all convert to 0x100. with -M but not -a, 0x100 is chimeric alignment.
see also"With 0.7.5 if read has a chimeric alignment, the paired or the top hit uses soft clipping and is marked with neither 0x800 nor 0x100 bits, All the other hits part of the chimeric alignment will use hard clipping and be marked with 0x800 if option "-M" is not in use, or marked with 0x100 otherwise." (; );Other hits part of a chimeric alignment are now reported in the SA tag, conforming to the SAM spec v1.5"

For Bwa-sw, in the manual it says that:'in the paired end mode, bwasw may still output split alignments but they are all marked as not properly paired;' so at least it is in the -F 2 filed, for chimeric alignment, maybe -f 0x100 or 0x800, for fusion, sorry, I do not know what does it mean.

you may also post your question on biostar or the mailing list of bwa on sourcefore.
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