Optimal aligner and variant caller
Hi
I'm analysing exome dataset, I performed the alignment and variant calling with different tools BWA-MEM, Bowtie2, Cushaw3, Novoalign. Variant calling by Freebayes and GATK-HC. How can I conclude which aligner is the best, on what parameters ? I feel, 1) Alignment percentage (no. of PE reads mapped against reference) 2) Computation time
Can you give me a strong answer.
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Here you have one part of the discussion : C: BWA MEM vs BOWTIE2 , which is best?.
What are your goals ? At the end if you point some deficiencies how you will confirmed it to know which is right ?
Hello pinninti1991reddy!
Please follow up on your questions. See C: Readgroups for a bam file ?
For this reason we have closed your question.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!