Converting a SAM file to a FASTQ file with picard

We can generate one (single-end) or two (paired-end) FastaQ files from a BAM file using Picard.

java -jar SamToFastq.jar 
    I=HG00096.chr20.sam 
    F=HG00096.chr20.1.fastq 
    F2=HG00096.chr20.2.fastq
Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: