Question

How Do You Convert A Sam/Bam File To A Psl Or Axt Format?

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11.3 years ago

lp364 ▴ 20

I am trying to make a chain file to use in liftOver and these can be made using PSL or AXT files. My current data is in SAM/BAM. What's the best way to convert this to a psl or axt format?

samtools conversion • 3.9k views

ADD COMMENT • link updated 11.3 years ago by Alex Reynolds 36k • written 11.3 years ago by lp364 ▴ 20

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cross posted on seqanswers: http://seqanswers.com/forums/showthread.php?p=112080#post112080

ADD REPLY • link 11.3 years ago by Pierre Lindenbaum 164k

score 0 · Answer 1 · 2013-07-30

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11.3 years ago

Alex Reynolds 36k

Perhaps you could try passing the output from the sam2bed script to the bed2psl.py script. I'd take care to make sure coordinate indexing is correct at each step of the process.

ADD COMMENT • link 11.3 years ago by Alex Reynolds 36k

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where can you download the bed2psl.py? It seems that the sam2bed doesn't process the cigar string that is needed to generate the psl.

ADD REPLY • link 11.3 years ago by lenore.pipes ▴ 20