Advantages of split by chromosome?
Hi, I'm a baby at this field, and trying to do some tutorials like GATK best practice, CNV analysis, HLA-typing etc.
I have a question about files that are split by chromosome.
What advantages do they have?
And If I use them, is my command correct like below?
ex) bwa mem REF_Chr1.fa A_1.fastq A_2.fastq > A.sam
After many process, do I have to merge them at the end?
Thank you!
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Pierre Lindenbaum
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kwanghoon •
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parallelisation.
No never map a bam on a contig only. you'll get false positives. You must use the whole reference genome.
Then do I need to split after bam processing using whole reference?
Sorry I have no knowledge.
you don't have to _split_ the bam. For example, for calling variants, most tools are able to call a specific region/chromosome if the bam is indexed (=bai file)