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March 9, 2017
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 allow for it).
It was quick as advertised by GATK:
Total runtime 237.36 secs, 3.96 min, 0.07 hours
Chr1 in rice is 40Mb.
Resulted in a vcf file. Here's an example of a SNP:
As you can maybe see, there are two sets of genotype fields:
Both SNPs are Het lets look for one that is Het in one and HOM_REF in the other:
SRR834927 0/1:44,6:50:99 :0|1 :48808_G_A:113,0,2424 SRR834931 0/0:27,0:27:0 : . : . :0,0,632
So first thing is that this SNP has new Genotype fields - PGT and PID. The tags are used to emit physical phasing determined by HC.
Reproducing Yang et al. - Chr1 Joint Genotyping
Reproducing Yang et al - HaplotypeCaller
March 8, 2017
Reproducing Yang et al - BQSR
March 6, 2017