bam size generated with stampy

[EricIngX]

Dear all,

I order to assemble genomes (20x, illumina paired end, Bos taurus) I did the 2 steps (see command below) indicated on the Stampy manual (bwa+samtools and next, remap with stampy). My question concerns the size of the files generated in both steps. For example, for a given genome, the first step (BWA+samtools) generates a file of only 68Go, and 45Go once sorted, while the remapping with stampy generated a file of 215Go (4 time bigger than the original sorted bam). So is it expected that this step (stampy remapping) may generate file 4 time bigger? Or does this indicate an error from myself (parameters, filtering?) or eventually a bad quality of sequencing?

Details of my commands:
step 1 : ("5. faster mapping with BWA"), I generated bam file with bwa & samtools:

bwa mem -t 4 -M $REFERENCE $FASTQ_PATH/$FILE\_R1.fastq.gz $FASTQ_PATH/$FILE\_R2.fastq.gz | samtools view -b -S - > $IO/$FILE.bam

step 2 : I remapped the BAM file using Stampy, and keep only well mapped reads:

stampy.py -g Bt -h Bt -t 8 -o $FILE\_StampyProcessed.bam --bamkeepgoodreads -M $IO/$FILE\_sorted_NODUP.bam

Thanks for the help!

[GenoMax]

It appears that your stampy bam may be sorted (based on the name) but perhaps the new bam has additional fields (see: http://seqanswers.com/forums/showthread.php?t=47843).

[EricIngX]

thanks for the help, but the solution was a bit embarrassing for me: I forgot to convert sam to bam, as Stampy produce only sam output! Sorry for that!