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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

Creating Panel of Normals Error

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    Genevieve Brandt (she/her)

    Hi Vincent Appiah, the contigs from gnomad and your reference will need to match. The reference contigs are named with "chr" and the features are just the number. You can use our tool LiftOverVcf (Picard) to change the names.

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    Vincent Appiah

    Thanks Genevieve Brandt (she/her) . I was able to do the lift over. However I had some logs which I was not quite clear when doing the lift over. Below is an extract

     


    INFO 2020-09-26 01:45:44 LiftOver Interval chr1:396626-396629 failed to match chain 381 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0)
    INFO 2020-09-26 01:45:44 LiftOver Interval chr1:396627-396630 failed to match chain 381 because intersection length 2 < minMatchSize 4.0 (0.5 < 1.0)
    INFO 2020-09-26 01:45:44 LiftOver Interval chr1:396628-396629 failed to match chain 381 because intersection length 1 < minMatchSize 2.0 (0.5 < 1.0)
    INFO 2020-09-26 01:45:44 LiftOver Interval chr1:417963-417965 failed to match chain 381 because intersection length 2 < minMatchSize 3.0 (0.6666667 < 1.0)
    INFO 2020-09-26 01:45:44 LiftOver Interval chr1:454973-455027 failed to match chain 381 because intersection length 54 < minMatchSize 55.0 (0.9818182 < 1.0)
    INFO 2020-09-26 01:45:44 LiftOver Interval chr1:455118-455119 failed to match chain 381 because intersection length 1 < minMatchSize 2.0 (0.5 < 1.0)
    INFO 2020-09-26 01:45:44 LiftOver Interval chr1:455443-455444 failed to match chain 381 because intersection length 1 < minMatchSize 2.0 (0.5 < 1.0)
    INFO 2020-09-26 01:45:44 LiftOver Interval chr1:456431-456433 failed to match chain 381 because intersection length 2 < minMatchSize 3.0 (0.6666667 < 1.0)
    INFO 2020-09-26 01:45:44 LiftOver Interval chr1:464465-464467 failed to match chain 381 because intersection length 1 < minMatchSize 3.0 (0.33333334 < 1.0)

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    Genevieve Brandt (she/her)

    Vincent Appiah these are examples of intervals that did not match your chain file. It is not an error message, so you can still proceed, but it may be something you want to examine.

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