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Should the number of SNPs stop changing between successive rounds of BSQR?
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
I can provide further information if it would be helpful.