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GVCFblocks

Hi gatkers!

I'm currently working with gvcf files, and there are some aspects that I dont better understand.
- In a non-variant block, do all the positions from POS to END have the same REF allele, for example , in a block of thousands of positions which an A as REF allele, are there thousands of adenines?
- In the gvcf file, will i have always all genome positions or could i filter it using a bed file/intervals of interest?

Any help is very wellcome.
Thank you very much!

Marta.
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Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @MartaWaters

    • In a non-variant block, do all the positions from POS to END have the same REF allele, for example , in a block of thousands of positions which an A as REF allele, are there thousands of adenines?

    Yes

    • In the gvcf file, will i have always all genome positions or could i filter it using a bed file/intervals of interest?

    You can filter by using intervals of interest

  • MartaWatersMartaWaters SpainMember
    Okey, great!

    Thank you very much
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