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running **bcftools stats -c both --fasta-ref $REF $VCF > $VCF.stats** fails although the fasta reference is the same used for mapping and calling the vcf.
looks like a IUPAC bug to me!
Is there a wa…
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Hi,
Can anyone help?
I'm using Sciclone since few weeks ago and now I want to include copynumber file into clustering.
Copynumber calls were made by VarScan2 and segmentation by DNAcopy accordingly…
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Sorry, I am curious to know which parameter must be set in the project.yam in order to run phylowgs and bubble tree?
thanks!
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i use the somatic command to call mutations, the num of forward and reverse strands diff greatly, the forward is usually much more than the reverse , and the total depth is also much less than other …
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I'm running hap.py like this:
hap.py patient_3_strelka.vcf.gz patient_3_varscan.vcf.gz --reference /b37/human_g1k_v37.fasta -o ${NAME}_str_var
My input vcfs are sorted, bgzipped, and tabix …
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Hi, thanks for the awesome tool and for the great support you give to your users.
I am trying to use the bcbio pipeline to call variants on a batch of all tumour samples. However when I try to use …
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As the subject says, [it was published in Genome Biology last year](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1029-6) and at least from the paper it looks interesting for sam…
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I’ve used the cnvkit a few times, but this particular sample results in stating everything is at a loss.
This is the head T1.cns file produced by bcbio (i removed the gene column for clarity)
``…
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Hi -
I am piloting some deep sequencing on human blood samples using unique molecular identifiers (UMIs). This is new for me, but I have previously done plenty of calling and annotation on hybrid …
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Hello, I'm getting an error during an ensemble pipeline for germline variant calling. It seems that the output of varscan is incorrectly being read by Bcbio, near the end of the whole process, when th…