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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Query regarding CombineGVCFs

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    Genevieve Brandt (she/her)

    Hi Abrish,

    Yes, this warning is totally fine. Here is more information about the MLEAC annotation (from the GVCF article):

    ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

    It is only calculated when there are alt alleles at a certain position. In your GVCF, you'll have sites with no alt alleles and so this annotation will not be present. If you want to double check that this is true, you can take a look at the position 10:1547 to see what that site looks like.

    Best,

    Genevieve

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    Abrish

    Hi Genevieve Brandt (she/her) ,

    Thank you so much.

    Sorry for the silly question, But where can I check position 10:1547. I should check it in vcf file?

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    Genevieve Brandt (she/her)

    No problem! Yes, it would be in your GVCF inputs. 

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    Abrish

    Dear Genevieve Brandt (she/her),

    Thank you so much.

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