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Hi,
I'm currently trying to call variants on a set of candidate genes (specified via `variant_regions`) for 63 WGS samples, and the 'callable regions' step is taking far too long.
Looking at the…
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We are starting to pull data that about 'molecular phenotypes' which inhere in molecular entities, activities, or processes. These include things like variants causing altered altered expression, act…
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Thanks for developing the cancereffectsizeR tools!
We are performing some genomic analyses comparing the patients before and after treatments. Could we use cancereffectsizeR to quantify differentia…
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1) Could non-coding exons interfere with the calculation of the $dist, $d variables in LoF.pm lines 257-263? The code is simply looping over exons in the gene (via perl sub get_gerp_weighted_dist), i.…
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Hello,
Is it possible to get multiple BAM files to appear while using the --track-config option?
My code chunk looks like this:
```
create_report \
--fasta $genome_fasta \
--output "${…
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It is difficult to guess the exact meaning of variants column of Mykrobe results. For some examples below
fabG1_C-15T-C1673425T:44:83:93
fabG1_T-8C-T1673432C:83:0:99999994
katG_W191G-CCA2155539CCC:…
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Would it be possible to print the strand information in the output? i.e. whether the variant is annotated to + or - strand of a specific gene?
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While running the following command:
```
apex cis \
--vcf /mnt/mfs/ctcn/datasets/rosmap/wgs/ampad/variants/snvCombined/DEJ_11898_B01_GRM_WGS_2017-05-15_1.recalibrated_variants.annotated.vcf.gz \
-…
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Hello,
I understand your explanation regarding why some variants are not scored, but none of the possibilities seem to explain why my variant is not scored. Do you have any suggestions?
NM_000455.5:…
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Hi,
I am working on converting variants of different formats to gDNA variants I found some items gave different results:
commandline (version : 2.3.4)
```
hanh@cpuserver:/data/home$ transvar p…