BWA or SMALT mapping algorithm

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9.5 years ago

P.NJ ▴ 50

I am using BWA for aligning targeted 'gene-pooled' exonic gene regions generated from Illumina 1.9 against whole genome human reference. The parameters I used for the command "aln" are

bwa aln -n 2 -q 15 -l 35 -t 8 -I

But I was just wondering if it is a good idea to disable the seeding and also change -n to 0.01 ? Also, my sequencing data is Illumina paired-end data (2x250 bp). So will other algorithms such bwa-mem or SMALT be better to use than bwa-aln?

SMALT BWA • 3.8k views

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by P.NJ ▴ 50

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Could you please describe "'gene-pooled' exonic gene regions" in more detail?

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by Biomonika (Noolean) 3.2k

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To explain it in simple words, DNA samples from cases and controls are combined together to form a population library and processed to produce sequence data for the defined target regions in the genes...

Any suggestions for my questions?

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by P.NJ ▴ 50

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bwa-aln does not work well for 250bp reads.

ADD REPLY • link 9.5 years ago by lh3 33k

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what would be an alternative then ?

ADD REPLY • link 9.5 years ago by P.NJ ▴ 50

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I probably would say bwa mem?

ADD REPLY • link 9.4 years ago by 14134125465346445 ★ 3.6k

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