SMALT aligner SAM clipping option?
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5.3 years ago
JstRoRR ▴ 60

I am mapping my reads using smalt (for specific reasons) program and I am wondering if any one have come across smalt's sam output formatting options? you can specify format output with -f flag. it also has some extensions i.e

-f sam:nohead:x:clip

where x is for cigar string, nohead is for no headers and clip is for hard clipping. I think smalt by default hard clip reads. its not mentioned anywhere what to use in case I dont want hard clipping? I tried values like no clip etc...but it doesnot work. Any ideas?

SMALT mapper sam hardclipping • 1.2k views
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