SAM spec / BWA-MEM

mozack

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Join Date: Jun 2013

Posts: 8
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#1

SAM spec / BWA-MEM

06-19-2013, 11:23 AM

Hello,

The release notes for bwa-mem 0.7.5 reference an upcoming SAM spec v1.5. Does anyone know if a preview of the coming spec changes is available publicly?

"Changed the way a chimeric alignment is reported (conforming to the upcoming
SAM spec v1.5). With 0.7.5, if the 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."

Thanks!
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BAMseek

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Join Date: Apr 2011

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#2

06-19-2013, 12:16 PM

I found the latex for it:

hts-specs/SAMv1.tex at master · samtools/hts-specs

https://github.com/samtools/sam-spec/blob/master/SAMv1.tex

Specifications of SAM/BAM and related high-throughput sequencing file formats - samtools/hts-specs

Looks like you'll have to convert latex to pdf if you want to make it more readable.

Justin
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