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is my pipeline correct to perform bqsr bootstrap with gatk4 ?
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 ?
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
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
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 !!