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edit readme to show how this can be ran to extract individual samples instead a group of samples. add default sge settings to the header of the script. add some documentation/comments in the script to…
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Hey, I am trying to do allele-specific expression analysis (ASE) for a few RNA seq samples ( 32 disease and 5 normal samples, unpaired unrelated). Could you suggest a pipeline/method to convert the ma…
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Hi,
I have been running InterVar to annotate my variants and I have realized that in the `annovar` subprocess, dbnsfp33a and dbnsfp31a_interpro are used, both of which add one column named `Inter…
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Can it take VCF from a GRCh38 analysis? Please suggest possible way to do.
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Hi,
I would like to download a number of files suggested in the tutorial. Eg. gnomad_exome. However, I got error message.
Command:
`annotate_variation.pl -downdb gnomad_exome humandb/ -build h…
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hi Developer,
I am bioinformatic from illumina in China.
So many dragen-customers(E.g:The First Affiliated Hospital of Zhengzhou University, China Yixueke Xueyuan Hemopathy Hospital) try to use …
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We're upgrading to the latest version of some databases but we are unable to download the IDX files for:
hg19_gerp++elem
hg19_avgwas_20150121
How can we index these databases or receive the idx…
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Hi,
I read with great interested your paper on ASEP.
Could you share code that you used to get your RNA-sequence data into an ASEP input data.frame/format?
yours,
Andrew
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Hello!
We have a few enhancement requests to make. Mainly concerning the outputs -
- HTML output to include variants of interest
- HTML output with population filtered variants
As it stands…
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Dear sir,
I use mutect2 to call the somatic variants and use filtermutectcalls to generate the FILTER field.
Finally, I use annovar to annotate the mutect2 output file and get three file(multianno.t…