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Old 06-23-2010, 01:02 PM   #1
foxyg
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Default HG18 or HG19?

Hi, guys, which one should I use to build index? Is HG18 more complete than HG19?
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Old 06-23-2010, 01:25 PM   #2
Jon_Keats
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Depends on your goal. Typically I would recommend using the newest genome version but you may have a situation that requires hg18, however, almost all applications/resources have now moved to hGRC37/hg19. The one issue seeing your other post is some versions of hg19 are to big for the BWA index step (see my intro post for description and options I found) also are you converting reads from illumina format to sanger format fastq? If not do so before you align.
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Old 06-23-2010, 01:35 PM   #3
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What is the difference between Illumina FASTQ format and Sanger format? I thought the only difference is offset.
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Old 06-23-2010, 01:50 PM   #4
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If you mean the Phred like quality score values, then yes you are correct the seemingly relevant issue is the scale/offset +33 versus +64 difference. But you need to convert to the sanger scale values or your variant calling will not work correctly.
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Old 06-23-2010, 01:53 PM   #5
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Thanks for the answers.

Lets say after I convert, if I want to use the -q option what is the best value to choose?
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