Wrong decription

[andreyurch]

Hello, It seems that command in the examples bwa mem -M example.fasta example.1.fq example.2.fq | samtools view - > example.bam

produces a SAM file instead of a BAM. To receive a BAM we need to use

bwa mem -M example.fasta example.1.fq example.2.fq | samtools view -Sb - > example.bam

[svm-zhang]

Hello @andreyurch,

You are absolutely correct. Thanks very much for pointing it out! I will update the README. :)

Simo

[svm-zhang]

Hello @andreyurch,

Samtools command line is now fixed :) Thanks!

Simo