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October 13, 2016
As I couldn't get the QTLseq framework to work because of perl version issues. I'm trying to follow some other examples and do the analysis step by step.
First we need to align the Gy 14 reads to the 9930 reference genome.
We'll use BWA 0.6.0 to align the reads, after they have been cleaned with trimmomatic (link). I'm following the manual here.
Like most aligners BWA needs to first create an index of the reference genome that you are aligning to.
That took about 3.5 minutes so I just ran it on the dev node.
Next step is to align the reads with bwa mem, which is the newest and preferred algorithm.
Testing the alignment quality with Picard tools.
I first sorted the sam file.
Then run the CollectAlignmentSummaryMetrics tool:
Where R=reference genome, I=input file and O=output file.
The definitions for the metrics can be found here.
Total reads: F- 21110117, R- 21109396
Reads Aligned: F - 19732408, R- 19727454
93.4% reads mapped!
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