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LucaB

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Latest activity by LucaB
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    LucaB commented,

    1. Community
    2. Germline
    3. HaplotypeCaller and SoftClipped bases

    Hi, The adapters were removed before aligning with BWA, and the clipped reads have no supplementary alignments. However, the clipped portions still align perfectly ~200 bases upstream. Beyond wheth...

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    LucaB created a post,

    HaplotypeCaller and SoftClipped bases

    1. Community
    2. Germline

    Hi,When analyzing a WES sample for variant calling, we observed a heterozygous SNV with an allele depth (AD) of 36,28 in the gVCF/VCF. However, upon inspection in IGV, only 3 alternative bases are ...

    • LucaB
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    • 3 comments
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    LucaB created a post,

    0 AD/DP for called variant in HaplotypeCaller

    1. Community
    2. Germline

    Hi, I am using GATK v.4.5.0.0. and calling variants with HaplotypeCaller. While investigating the minimum variant allele frequency called by HaplotypeCaller, I noticed that some variants are called...

    • LucaB
    • 2 followers
    • 1 comment
    • 0 votes