The re-calibration (BQSR) step didn't finish. I will use the on-the-fly capacity in HaplotypeCaller (HC) to apply the BQSR. 

I am also trying to use the g.vcf pipeline for the first time. It is not really necessary but I want to see what the output is and wanted to give...

So since this paper is doing QTLseq in rice I decided to take advantage of the fact that rice has a dbSNP database.

I want to see if I can run BQSR with a merged rice dbSNP file I received from a colleague.

So first thing I found out was that the contigs in the two files...

I was happy with the BQSR bootstrapping results. 

It seemed that after two rounds of bootstrapping we reached convergence, i.e. the correct quality scores were not changed much after the second round.

Variant quality score distributions:

However, bootstrapping BQSR is mea...

Ok so once the bases have been calibrated using a bootstrapped BQSR, variants have been called on calibrated data, snps and indels filtered and combined..... we can now make the Gy_genome.fasta.

Using FastAlternativeReferenceMaker (still part of GATK).

Edit 10/31/16

Make...

From GATK tutorial:

"Variant calling algorithms rely heavily on the quality scores assigned to the individual base calls in each sequence read. These scores are per-base estimates of error emitted by the sequencing machines. Unfortunately the scores produced by the mach...