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Dear Eric,
The cn-filter of the call module crashes quite a number of my samples when processing chrY. I have not been able to figure out when exactly this happens. All I can say is that I have onl…
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Hi,
is the estimation of genotype probabilties from posterior SAF's (instead of MAF's) already working or still in development? When I run the following command I get a segmentation fault:
> ang…
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The following one-liner (which I Googled, so I cannot vouch that this is the best way to do things) revealed 245Mb of files that are unused in master:
for ff in `find src/test/resources -name "…
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It looks like the samtools mpileup doesn't do the job.
Any ideas ?
> samtools mpileup -C 50 -v -l 23andMe_V3_hg19_ref.tab.gz -f hs37d5.fasta 1.bam > 23andMe_raw.vcf.gz
samtools :
> $ samtoo…
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Hope this helps!
The VCF below throws an error. It has a single sample. Trigger the error by running:
```
from cyvcf2 import VCF
v = VCF("in.vcf")
for record in v:
record.gt_bases()
``…
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Hi,
this seems could be a bug in vcftools-0.1.14 not removing entries with INFO field being INDEL. Seems the annotation stems from bcftools-1.2 which did the initial SNP callling.
Anyway, I am…
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```
balter3:~$ conda create --name pysambcf
Fetching package metadata .................
Solving package specifications:
Package plan for installation in environment /home/Applications/conda/envs/p…
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Hello,
I try to detect association using already computed GL files like beagle.gz or glf.gz .
As i have some quite heavy bam-files, i thought i can skip the processing of them (takes about 2 day…
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Any plan on this? Thanks
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Hello,
I have problem during installation - after adding all depencies (Htslib and Eigen), I am able to perform cmake step with this output:
```
-- DeNovoGear version is 1.1.1-unknown
-- Boost…