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is my pipeline correct to perform bqsr bootstrap with gatk4 ?

chloe_teamMycochloe_teamMyco France, LyonMember

Hello gatk team,

I'm confused because I have no idea about the exact pipeline to use to perform bqsr bootstrap in order to have my final_recalibrated.bam and do my variant calling.
I was familiar with the pipeline of gatk3.5 but not at all with the version 4...
Some threads tell to always use the original sample.bam file to perform bqsr bootstrap and some others use sample_recaln.bam file ….
And know I got lost.

is the Following pipeline correct ?

1rst round

sample.bam + HaplotypeCaller --> sample_recal0.vcf

sample_recal0.vcf + vcftools --> sample_filtreted_recal0.vcf

sample_filtreted_recal0.vcf + sample.bam + BaseRecalibrator --> sample_recal0.table

sample.bam + sample_recal0.table + ApplyBQSR --> sample_recal0.bam
2nd round**

sample_recal0.bam + HaplotypeCaller --> sample_recal1.vcf

sample_recal1.vcf + vcftools --> sample_filtreted_recal1.vcf

sample_filtreted_recal1.vcf +** sample.bam ** (correct ? or should I use sample_recal0.bam) + BaseRecalibrator --> sample_recal1.table

**sample.bam **+ sample_recal1.table + ApplyBQSR --> sample_recal1.bam

3rd round

and so on until convergence ??

As soon as I reach convergence I run ApplyBQSR with my sample.bam file and the sample_recalN.table then HaplotypeCaller ?

Thank's a lot in advance to solve my issue and to allow me to understand how bqsr works in gatk4 with samples with no known snp nor indel !!


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