Convert Sam2Psl Or Sam2Axt?

Question

[2184687-1231-83-]

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?

[Vitis]

Is it possible to use awk?

[Sean Davis]

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?

[2184687-1231-83-]

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

[Sean Davis]

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

[Aleksandr Levchuk]

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

Answer 1

[pratibhamani]

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.