SEQanswers - View Single Post - pileup output different using Maq and Samtools commands

colindaven · 03-31-2011, 04:05 AM

I would use Samtools as it is under active development and Maq, to my knowledge, is not any more.

However for SNP calling try the mpileup pipeline described on the Samtools webpage instead of using pileup. It's important to generate the I16 info fields for variant calling in our experience.

03-31-2011, 04:05 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	I would use Samtools as it is under active development and Maq, to my knowledge, is not any more. However for SNP calling try the mpileup pipeline described on the Samtools webpage instead of using pileup. It's important to generate the I16 info fields for variant calling in our experience.