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I updated bcbio to use the more robust dbNSFP VEP annotation and am getting an error I haven't seen before.
[2017-02-06T18:02Z] Ensemble consensus calls for Kindred_87: samtools,platypus,gatk-hap…
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Using the VCF plugin. Variants are called by [freebayes](https://github.com/ekg/freebayes) and then annotated with VEP. Multiple fields seem to be missing here that are present in the VCF, but in alte…
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Hello,
I am performing CNV analysis on DNA data. Here is my configuration file:
``` details:
- analysis: variant2
genome_build: hg19
algorithm:
mark_duplicates: true
recalibrate…
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Short: Nothing appears in Peripheral tab on debug with ATSAMD10/OpenOCD/CMSIS-DAP; why?
Longer:
I have installed the tools on Windows (10).
Installed:
GDB Hardware 8.8.0
Eclipse 4.5.1
Packs 2.2.2.2…
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Hi
I've just used the copywriteR package to analyze a tumour-normal pair. After the execution I have run the `plotCNA` function as described. The output is that I should re-analyze the sample because…
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The nugget of code below works beautifully:
``` python
import vcf
vcf_reader = vcf.Reader(open('../SNPs/snps_spretus_chr19.recode.vcf.gz', 'r'))
snps_vcf = vcf_reader.fetch('19', 0, 200000000) …
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I have a bed file as follow:
chr1 69090 70008 OR4F5
chr1 367658 368597 OR4F29
chr1 621095 622034 OR4F16
chr1 861321 879533 SAMD11
chr1 880073 894620 NOC2L
I used the follow…