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

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
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updated by Alex Reynolds Alex Reynolds • written by lp364 • lp364

1 answer

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.

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written by Alex Reynolds Alex Reynolds

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.

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written by lenore.pipes • lenore.pipes

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