SNP finder

[roshanbernard]

HI,

i need a help in fininding out the SNP in while genome.. i have whole genome sequence of .acidophilus strain. mutant strain and wild type...which software i can use to find the SNP among this two whole genome sequence...


regards

roshan

[AsoBioInfo]

there are many softwares like SNP detector, SNP browser. although I havent used anyone but just heard their names.

[roshanbernard]

Thanks for ur reply..i tried using SNP detector...however it was pretty hard for me operate it..so i was wondering if any other software available...

[yqzhu]

Samtools is an excellent software to find NGS snps.

[roshanbernard]

thanks a lot :-)...this is helpful to me

[dahlo]

Bwa + gatk

Hello there

A college of mine did a lot of comparison between different combinations of aligners and SNP callers. If i remember correctly, he found that aligning the reads with BWA and using GATK to detect SNPs was the best way to go.

I did not see any numbers on it, just heard it at the coffee table But i could be worth checking out if you have not looked at them before.

This was on human samples i might add.