Hello,
I would like to know if there is any tool to convert SOAPsnp to SOAP? Once it is converted to SOAP, I can convert it to SAM using Soap2Sam from reseqtools. Hopefully using reseqtools is not that complicated.
If this is complicated, i wouldn't mind trying the reverse. Somehow converting SAM file to SOAPsnp files.
Background: I ran BWA in a HPC cluster. So I have SAM/BAM files from that test. Now I have to generate SAM/BAM files from the same data by running tests on Hadoop/AWS. I tried using DistMap. But ran into some errors; still trying to fix those errors. Now I am thinking of using Crossbow, which seems to be relatively easy to run on AWS. After that I have to compare both the results in terms of quality, time etc.
Hoping to find some help from Biostar members.
Thanks, Ashwin