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Old 05-13-2011, 06:58 AM   #1
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Join Date: Aug 2009
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Default SAMTOOLS AND GATK input file (base qualities)

I started off with Illumina qseq format - converted to fastq.
I used the sol2std conversion from Maq and used the fastq to align against reference using BWA.
Used the original qseq files to align against reference using ELAND.
I got the output of BWA in SAM format and ELAND in export (which I converted to SAM using
Now, the purpose is to detect SNPs and indels using samtools which expects (or interprets) the base qualities in a particular phred scale (Phred+33 correct?).
Could someone help me sort the out the base quality scales in these file formats and what is the correct way to format the input SAM files before running pileup?
Same question for GATK unified caller - what kind of base qualities should I ensure is in the input SAM files?
If I use a standard converter such as sol2std or export2sam how can I be sure the base qualities are in the correct scale?

Thanks in advance.
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