Genome Analysis Toolkit

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

other reference in BaseRecalibrator known-sites option

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    BI_joy

    add

    when I did LiftoverVcf, it has the error

    log

    ...

    INFO 2020-10-08 16:07:28 LiftOver Interval chr1:108359162-108359163 failed to match chain 1069 because intersection length 1 < minMatchSize 2.0 (0.5 < 1.0)
    INFO 2020-10-08 16:07:28 LiftOver Interval chr1:108371701-108371702 failed to match chain 1075 because intersection length 1 < minMatchSize 2.0 (0.5 < 1.0)
    [Thu Oct 08 16:07:28 KST 2020] picard.vcf.LiftoverVcf done. Elapsed time: 6.52 minutes.
    Runtime.totalMemory()=12119441408
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
    at java.lang.String.checkBounds(String.java:383)
    at java.lang.String.<init>(String.java:324)
    at htsjdk.samtools.util.StringUtil.bytesToString(StringUtil.java:301)
    at picard.vcf.LiftoverVcf.tryToAddVariant(LiftoverVcf.java:558)
    at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:453)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:301)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

    thank you

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    Genevieve Brandt (she/her)

    BI_joy you will need a valid chain file from GRCh38 to the reference you are using to get this to work. 

    Here is a good explanation from UCSC: http://genomewiki.ucsc.edu/index.php/LiftOver_Howto

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    BI_joy

    Genevieve Brandt (she/her) Thank you for letting me know.
    I will refer to it and study.

    thank you

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