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Reproducing Yang et al. - Chr1 Joint Genotyping
March 9, 2017
Reproducing Yang et al - HaplotypeCaller
March 8, 2017
Reproducing Yang et al - BQSR
March 6, 2017
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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...
December 12, 2016
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...
December 11, 2016
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...