Hi, Happy new year.
Can GATK handle multiple nucleotide mutation like TTT>AAA
Or deletion insertion events like : c.2839-3_2839-1delinsGATACTA
And what is the max length of indel called by GATK?
Automatic MNP merging may have been turned off a while back.
You can try using the --mergeVariantsViaLD flag.
You can also try running Read Backed Phasing after Haplotype Caller with the -enableMergeToMNP flag https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_phasing_ReadBackedPhasing.php#--enableMergePhasedSegregatingPolymorphismsToMNP
Happy New Year to you too!
Yes, GATK can handle multiple nucleotide mutations and deletion insertion events like you posted.
The maximum length of an indel called by GATK is the size of the active region. The default size is 250, but you can change it with the --activeRegionMaxSize argument. https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php#--activeRegionMaxSize
In the vcf files I seen from GATK, I never met the multiple nucleotide mutations and deletion insertion events Is there suppose to switch some kind of options on?
Can you post an example record? Also, please post the IGV screenshot of the region. You should not need to turn on any special flags.
I wonder if GATK can detect Trinucleotide repeat?
Yes, GATK can detect trinucleotide repeats.