How To Process Soapalign Results Before Call Snps And Indels By Samtools?

Question

[Haiping]

Hi. I want to use SOAP to align my data to references and then call SNPs and Indels by using Samtools. Problems is that there are two output files related to pair aligned reads and single aligned reads produced by soap. So how to ideal with this two files before I use samtools? I tried to just combine two files by cat command but I am not sure if it will influences the final results. So is there any suggestions? Thanks.

Answer 1

[lh3]

There is a soap2sam.pl script in samtools, but I would suggest you change to another mapper that native supports SAM output. Recommended: bwa, novoalign or stampy.

[Haiping]

Thanks. Actually I do hava novoalign resutls. I just want compare the results between soap and novoalign.

[lh3]

Novoalign is almost certainly better. No need to compare in fact.

[Haiping]

Haha.OK. Thanks.