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How can i do alignment to my fastq data?

I got several fastq data, and i just read some pipeline you guys released here.
And i don't which way is better to do alignment.
One way should be like this:
i should convert the fastq data into ubam, then i just use the picard's SamToFastq and bwa to do the alignment jobs. After that, i think i should use MergeBamAlignment to merge my sam file. Then i can use picard's MergeSamFiles or samtools to merge all my sam files.
The other way should be like this:
i just use the bwa to align my fastq file into bam file, and i just use picard's MergeSamFiles or samtools to merge them.

which is better? Dose these two ways get huge difference?

Thanks a lot !!!

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