find tandem repeats in DNA from CRAM/VCF file

Question

[anubratadas]

I want to find tandem repeats in DNA. I have access to CRAM file and the VCF file. I initially tried to get the insertions from the VCF file, but I am not sure if the variant caller has included all the repeats and if that is the correct strategy. So I want to find these repeats in the CRAM file also, to be certain. are there any packages for this?

one approach suggested was that i use samtools mpileup to create a consensus sequence and then search for tandem repeats. would this be an appropriate strategy?

I am new in this kind of analysis and will be very thankful for your help

Answer 1

[Pierre Lindenbaum]

search for STR in github: eg. https://github.com/quinlan-lab/STRling , https://github.com/Illumina/ExpansionHunterDenovo , etc ... and in pubmed...

[anubratadas]

Thanks a lot Pierre