Converting format insurance

[papori]

Hi all,
Probably this is a FAQ, but still i didnt find a good answer..

I am converting from bam to fastq.
My bam's are paired end, coordinated sorted and very large (100Gb+).
For my analysis i need only the first pair.

Right now i am using these 2 commands:

For converting bam to sam for the first pair.

samtools view -h -f 0x0040 $line > $line.pe1.sam

and for parsing the fastq from the sam format.

cat $line.pe1.sam | grep -v ^@ | awk '{print "@"$1"\n"$10"\n+\n"$11}' > $line.pe1.sam.fq

this i took from:

http://www.cureffi.org/2013/07/04/how-to-convert-sam-to-fastq-with-unix-command-line-tools/

How can i be sure that i got all the reads? mapped + unmapped of the first pair?

Thanks,
Pap

[maubp]

Samtools does (now) have a BAM to FASTQ option, that might be easier.

[papori]

Samtools does (now) have a BAM to FASTQ option, that might be easier.

Thanks maubp!!