How To Convert A Soapsnp Output File To Soap, Sam Or Bam Formats

Question

[bashwin.u]

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

Answer 1

[Istvan Albert]

The SOAPsnp program' purpose is to assemble a consensus genome based on alignments and a reference genome.

The output of the SOAPsnp program cannot be converted to an alignment format.

[bashwin.u]

Thanks for replying. Then I will have to think about converting SAM file generated from BWA to Soapsnp to do a comparison of both architectures. I understand I can convert SAM to SOAP by using reseqtools. But I am not too sure how to convert it to SOAPsnp. I think I can do that by sorting the SOAP file using msort and then use SOAPsnp. Is this how I can do?