Indelrealignment step is require further processing the bam file ?

Question

[sunnykevin97]

Hi

If I'm using GATK4.0, Indelrealignment step is required to process the bam ?

[WouterDeCoster]

Read the fantastic manual

[sunnykevin97]

How can i get known indel_calls.vcf to perform Indelrealigner step for bam files ?

-known /path/to/indel_calls.vcf

[sunnykevin97]

I'm looking for Mills_and_1000G_gold_standard.indels.hg38.vcf ?

[Kevin Blighe]

Where have you seen that file-name previously? Are you following a tutorial?

You have to provide more details in your comments.

[finswimmer]

Hello sunnykevin97 ,

please read the link WouterDeCoster carefully.

Note that indel realignment is no longer necessary for variant discovery if you plan to use a variant caller that performs a haplotype assembly step, such as HaplotypeCaller or MuTect2. However it is still required when using legacy callers such as UnifiedGenotyper or the original MuTect.

As you asked for GATK4 you probably will use HaplotypeCaller for variant calling. UnifiedGenotyper is longer recommended and is not part of GATK4 anymore.

So stop thinking about this step and where to find necessary files and go on in your analyses.

fin swimmer

[sunnykevin97]

thanks! If I'm during variant calling using Freebayes, strelka2 and other variant callers then Indel realignment is not necessary step ?

[finswimmer]

freebayes also performs a haplotype assembly step. So here you definitely don't need indel realignment.

You should keep in mind that the indelrealigner was designed to work within a gatk based pipeline. So I would be skeptical if this also works good with other tools.