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  • slny
    Member
    • Mar 2011
    • 54
    #1

    Error in VCF annotation with Gvanno

    Below is the command I used to run Gvanno:
    ./gvanno-1.3.0/gvanno.py ./sample.hard.filtered.vcf.gz --container docker ./gvanno-1.3.0 ./gvanno-1.3.0/examples grch37 ./gvanno-1.3.0/gvanno.toml out

    The VCF file was processed with bgzip and tabix to generate .gz and .gz.tbi files.

    The species is human.

    Below is the error message, which has thousands of lines. Only a few line are shown here:

    ......
    ERROR: Line 804858: Sample #1, GP=5.6646e+00,1.3750e+00,5.1170e+01 value does not lie in the interval [0,1].
    ERROR: Line 804859: Sample #1, GP=2.2889e+02,2.3590e+01,1.9344e-02 value does not lie in the interval [0,1].
    ERROR: Line 804860: Sample #1, GP=1.0629e+01,3.4093e+00,3.3991e+00 value does not lie in the interval [0,1].
    ERROR: Line 804861: Sample #1, GP=2.2913e+02,1.5194e+01,1.3340e-01 value does not lie in the interval [0,1].
    ERROR: Line 804862: Sample #1, GP=8.9898e+01,6.9973e+00,9.6757e-01 value does not lie in the interval [0,1].
    ERROR: Line 804863: Sample #1, GP=4.5184e+00,1.8937e+00,4.2228e+01 value does not lie in the interval [0,1].
    ERROR: Line 804864: Sample #1, GP=1.0629e+01,3.4093e+00,3.3991e+00 value does not lie in the interval [0,1].
    ERROR: Line 804865: Sample #1, GP=1.0629e+01,3.4093e+00,3.3991e+00 value does not lie in the interval [0,1].
    ERROR: Line 804866: Sample #1, GP=1.3753e+01,4.9465e+00,1.9547e+00 value does not lie in the interval [0,1].
    ERROR: Line 804867: Sample #1, GP=1.3494e+01,4.9576e+00,1.9667e+00 value does not lie in the interval [0,1].
    ERROR: Line 804868: Sample #1, GP=1.3544e+01,4.9554e+00,1.9643e+00 value does not lie in the interval [0,1].
    ERROR: Line 804869: Sample #1, GP=5.2025e+01,4.7513e+00,1.7717e+00,8.6795e+01,3.9521e+01,8.9795e+01 value does not lie in the interval [0,1].
    ERROR: Line 804870: Sample #1, GP=1.0629e+01,3.4093e+00,3.3991e+00 value does not lie in the interval [0,1].
    ERROR: Line 804871: Sample #1, GP=6.1242e+01,9.4986e+00,5.1722e-01 value does not lie in the interval [0,1].
    ERROR: Line 804872: Sample #1, GP=1.0629e+01,3.4093e+00,3.3991e+00 value does not lie in the interval [0,1].
    ERROR: Line 804873: Sample #1, GP=1.3747e+01,4.9467e+00,1.9549e+00 value does not lie in the interval [0,1].
    ERROR: Line 804874: Sample #1, GP=3.4071e+00,2.6492e+00,3.6393e+01 value does not lie in the interval [0,1].
    ERROR: Line 804875: Sample #1, GP=5.6071e+00,1.3973e+00,4.0161e+01 value does not lie in the interval [0,1].
    ERROR: Line 804876: Sample #1, GP=6.8343e+00,1.0096e+00,4.0008e+01 value does not lie in the interval [0,1].
    ERROR: Line 804877: Sample #1, GP=6.7787e+00,1.0242e+00,4.0022e+01 value does not lie in the interval [0,1].
    ERROR: Line 804878: Sample #1, GP=3.6677e+00,2.4399e+00,4.6070e+01 value does not lie in the interval [0,1].
    ERROR: Line 804879: Sample #1, GP=5.0772e+01,4.7783e+00,1.7581e+00 value does not lie in the interval [0,1].
    ERROR: Line 804880: Sample #1, GP=1.0629e+01,3.4093e+00,3.3991e+00 value does not lie in the interval [0,1].
    ERROR: Line 804881: Sample #1, GP=7.7499e+00,3.8146e+00,3.8046e+00 value does not lie in the interval [0,1].
    ERROR: Line 804882: Sample #1, GP=5.6067e+00,1.3971e+00,4.4142e+01 value does not lie in the interval [0,1].
    ERROR: Line 804883: Sample #1, GP=5.6087e+00,1.3982e+00,3.4693e+01 value does not lie in the interval [0,1].
    ERROR: Line 804884: Sample #1, GP=8.5678e+01,2.4012e-02,2.2586e+01 value does not lie in the interval [0,1].
    ERROR: Line 804885: Sample #1, GP=5.9799e+01,1.5572e-02,2.4464e+01 value does not lie in the interval [0,1].
    ERROR: Line 804886: Sample #1, GP=6.5573e+00,1.8855e+00,8.8221e+00 value does not lie in the interval [0,1].
    ERROR: Line 804887: Sample #1, GP=2.7122e+01,8.4333e-03,1.3260e+02 value does not lie in the interval [0,1].
    ERROR: Line 804888: Sample #1, GP=1.3570e+01,4.9543e+00,1.9631e+00 value does not lie in the interval [0,1].
    2020-06-21 04:18:04 - gvanno-validate-input - ERROR -

    Can anyone help ,me to resolve the problem?

    Thanks,
    slny
    Tags: vcf annotation gvanno
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