Should the number of SNPs stop changing between successive rounds of BSQR?

DuncanTormeyDuncanTormey Kansas City Member

Hello,

I am currently using GATK (GenomeAnalysisTK-3.3-0) to assess the level of heterozygosity in individual lizards (diploid). There is no known set SNPs or INDELs, so I have been using the bootstrapping protocol recommended in the best practices. Based on the recalibration plots, it appears that the before and after quality scores have converged, however the total number of filtered SNPs continues to change for each iteration of recalibration.

Should we expect the number of filtered SNPs to stop changing as we continue to bootstrap? Or should I be concerned about my dataset...

Some basic information:
We are using the unified genotyper for variant calling.
We have now completed 10 rounds of recalibration.
We are counting the number of SNPs that pass filtering

If I count the number of SNPs in unix:
for file in *.recode.vcf; do echo $file; cat $file | grep -v "#" | wc -l; done

all_SNPs_4.recode.vcf
922016
all_SNPs_5.recode.vcf
929913
all_SNPs_6.recode.vcf
923369
all_SNPs_7.recode.vcf
922344
all_SNPs_8.recode.vcf
923250
all_SNPs_9.recode.vcf
924366

I can provide further information if it would be helpful.

Thanks,
Duncan Tormey
[email protected]

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