I created a Chr1 g.vcf for both bulks. I want to see the results from joint genotyping.

Make the Chr1 vcf:

 Then used GenotypeGVCF to genotype.

Note the -stand_call_conf 30 option, which is performed in this step and not in the HC step (the -ERC GVCF function doesn't allo...

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'm working on reproducing results from a paper using my methods.

Make bwa index of Nipponbare v7:

Turns out there are some fasta formatting mistakes in the nipponbare ref...

Correct them:

 Prep the file for GATK:

 I processed the raw reads for alignment:

And aligned (o...

I wanted to download some data to reproduce results from a paper. 

Downloading from SRA sounds easy but it is actually really not straightforward...

I started by just downloading the files it took more than 10hrs and the read names were all messed up.... something didn't...

After making new bam files with altered read groups - now samples from two seasons share the same Read Group SM (Sample) tag - we can try calling variants as if they both came from the same biological sample but each was a different library.

Note, I forgot to index the...

I would like to run my GATK snp calling on two bam files as if they were one biological sample. 

There are a two recommended ways of doing this (mentioned here), and since I have already done BQSR I have decided to try the second way. 

I just need to change the read grou...

I wanted to learn how to submit jobs when the previous step in the pipeline is done. 

There is a method that uses

But that doesn't seem to work on MSU's HPCC.

The other way to do this is link:

so for my pipeline It would look like this

And would be run like so: 

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 now that an alternative reference fasta is made we can align the other samples to it.

qsub bwa-v.sh -v FILE=***

and then sort and dedup the sams:

qsub picard_sort_dedup-v.sh -v REF=*****.fasta -v NAME=***_aln