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This is something to keep in mind when we start using this functionality.
_Originally posted by @jPleyte in https://github.com/GenomicsDB/GenomicsDB/pull/186#discussion_r794222104_
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If you are wedded to using Deflate, don't use Zlib as it's simply ancient technology. I'd advise [libdeflate](https://github.com/ebiggers/libdeflate/) instead as generally it's over double the perfor…
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Apparently when we wrote the code for `vg chunk` haplotype tracing, we thought that all graphs would have one ID increment per node along whatever path we're using to define our region of interest. We…
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Hi,
I'm currently working on benchmarking VCF files generated from HG002_data(test_run just one sample) for SV calling(Manta, lumpy, GRIDSS, nf-core/sarek) against a truth set. I aligned the BAM file…
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Hi Simon,
referring to your paper here (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814882/), I have done a similar comparison between autosomal data and haploid sex chromosome data (homogametic in…
foala updated
4 years ago
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`writeVcf` performs some unnecessary work that interferes with a perfect roundtrip of a `VCF` to a file and back. At the very least, these discrepancies interfere with my unit tests that check for cor…
LTLA updated
10 months ago
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Hi Heng,
Great tool. Do you have any advice for joint calling of multiple samples?
I obtained a reasonable looking call set by first running your `run-calling` script on each sample individually. …
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```
import pysam
fp = pysam.VariantFile('0.9.29.eval.vcf.gz', 'r')
hdr = fp.header.copy()
print(hdr)
...
##contig=
##contig=
##FILTER=
##INFO=
##INFO=
##FORMAT=
##FORMAT=
##FORMAT=
##…
ghost updated
2 weeks ago
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vcf file:
##fileformat=VCFv4.2
##FORMAT=
##FORMAT=
##FORMAT=
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL
2 220439700 . G GCT . . . GT:AD:DP 0/1:21,72:93 0/0:51,0:51
3 52437426 …
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This is a feature request or, alternatively, a request for advice.
The ability of breseq to compare different samples in an HTML file is super useful. I am wondering how to use that information for…