Local realignment around indels

Question

[Elisa]

Hi everyone,

I'm new in bioinformatics field. I'd like to know how to and which are the best tools for local realignment around indels. I have fastq files coming from MiSeq (Illumina) as pipeline input and I'm performing the bioinformatic pipeline using python (and running tools from comand line). I should perform local realignment only after PCR duplicates removal? And which tool should I use to first identify indels around which local realignment will be done?

Thanks in advance, Elisa

Answer 1

[Pierre Lindenbaum]

I should perform local realignment only after PCR duplicates removal?

if you're calling the variant with GATK4, you don't need to realign the indel because haplotypeCaller will do it on the fly. Realignment disappeared in gatk4

[Elisa]

I was calling the variants with bcftools. Do you suggest me to use GATK4 instead? (I have a targeted sequencing problem with tumor samples)

[Pierre Lindenbaum]

when publishing it's (sadly?) better to say you used the "GATK best practices" to call your variants...