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GATK3.8 vs GATK4.1 - ready for analysis BAM-files

medgenmedgen NorwayMember

I have seen discussions indicating that it is not good to combine GATK 3.8 vs 4.1 intermediate pipeline-steps;
I have saved several recalibrated "ready-for-analysis" bamfiles (v3.8 -after printreads), and have produced several new ones ("ready-for-analysis") with ApplyBSQR (GATK 4.1).
a) is it OK to use Hapotypecaller on both these "ready-for-analysis" 3.8- and 4.1-generated bam-files and make g.vcf-files that can be combined in a common vcf-file?
b) I also have many 3.8-g.vcfs; Is it OK to combine g.vcf-files produced by haplotypecaller v.3.8 With recent g.vcfs With haplotypecaller v4.1?

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  • medgenmedgen NorwayMember

    Thanks. But concerning combining 3.8 and 4.1 g.vcfs; does "might cause errors"- mean that if I do not get an error message in the process of combining them it is probably OK? If not I go back to the bam-files and do the work once more to be sure ;-)

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    @medgen

    That is correct.

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