Do BAMs output by giraffe require indel realignment?

[jdidion]

Based on the methods in the Draft Human Pan-Genome paper (https://www.biorxiv.org/content/10.1101/2022.07.09.499321v1) it looks like BAM files surjected from giraffe graph alignments (which it appears can now be done directly by giraffe without the separate surject step) were indel left-aligned (using freebayes bamleftalign) and re-aligned (using GATK and ABRA). Is this still necessary, or have recent changes to giraffe obviated this step? I ask because I do not see it mentioned in the tutorial (https://github.com/vgteam/vg/wiki/Mapping-short-reads-with-Giraffe). If the step is still required, can Glia be used to replace bamleftalign/GATK/ABRA?

Thanks!

[hxt163]

Based on the methods in the Draft Human Pan-Genome paper (https://www.biorxiv.org/content/10.1101/2022.07.09.499321v1) it looks like BAM files surjected from giraffe graph alignments (which it appears can now be done directly by giraffe without the separate surject step) were indel left-aligned (using freebayes bamleftalign) and re-aligned (using GATK and ABRA). Is this still necessary, or have recent changes to giraffe obviated this step? I ask because I do not see it mentioned in the tutorial (https://github.com/vgteam/vg/wiki/Mapping-short-reads-with-Giraffe). If the step is still required, can Glia be used to replace bamleftalign/GATK/ABRA?

Thanks!

hello,i want to know if the problom has been solved.Can vg-surject-deepvariant pipeline without realignment step? Thank you!