Hi all,
A while ago I generated a single-sample VCF via HaplotypeCaller (v2.5 or v2.8), and we found a great candidate variant, with lots of read depth support. Now after some time i've redone this analysis with HC v3.1, now using joint calling, and the variant has dissapeared. To rule out the impact of HC v3.1, i called the single sample with HC v3.1 and the variant is again found.
I've attached GenomeBrowse screenshot, where the bottom 2 tracks show the strong read depth supporting the variant, and that the variant does exist in the single-sample VCF. the top track shows that the variant is missing from the multi-called VCF.
given that the new HaplotypeCaller "is so sensitive that it cries at the movies" (Broad's words not mine), i'm perplexed why such a strong variant didn't make it through the multicalling.
Has anyone seen similar, or better yet have an explanation?
cheers,
mark
A while ago I generated a single-sample VCF via HaplotypeCaller (v2.5 or v2.8), and we found a great candidate variant, with lots of read depth support. Now after some time i've redone this analysis with HC v3.1, now using joint calling, and the variant has dissapeared. To rule out the impact of HC v3.1, i called the single sample with HC v3.1 and the variant is again found.
I've attached GenomeBrowse screenshot, where the bottom 2 tracks show the strong read depth supporting the variant, and that the variant does exist in the single-sample VCF. the top track shows that the variant is missing from the multi-called VCF.
given that the new HaplotypeCaller "is so sensitive that it cries at the movies" (Broad's words not mine), i'm perplexed why such a strong variant didn't make it through the multicalling.
Has anyone seen similar, or better yet have an explanation?
cheers,
mark
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