Convert Sam2Psl Or Sam2Axt?
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10.4 years ago

I've googled for sam2psl and found a couple of references to it, but I actually think they are referring to psl2sam, other way around.

Has anybody got any idea if there is a sam2psl or sam2axt tool somewhere as part of a package or as a simple script?

sam blat samtools • 1.8k views
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Is it possible to use awk?

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Just curious, but what is it that you want to do with the psl-format file? Perhaps there is a tool that will do the same thing with SAM?

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@Sean Davis: this is to run axtChain on the resulting file. Both psl or axt would do.

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My guess is that you will have to write something yourself. In the end, it may be faster to simply realign with blat.

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Could any of the following help: sam2hmmer, sam2psi, sam2vcf.pl?

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9.6 years ago

I have the same issue. I want to convert SAM/BAM file to BLAT PSL file format. I found the psl2sam in samtools. Has anyone found an answer to this? Please help.

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