-
・VCFファイルのサンプルが欲しい(ダウンロードして見えるもの)。
・「アノテーション」ってなんでしょう?という質問をよく受けるので、アノテーションする前と、した後どういった形になるかがわかるもの(annovarでアノテーションをしたものが嬉しい)。
・上記の関係もあるので、VCFのサンプルはより現実的なデータが嬉しい気がする。CCLEのexomeのmutation callの結果をVCF変換…
-
Hi,
I have used the tool to annotate and filter variants. My question is how to replace the "_" (hyphen) to the actual bases in a avinput vcf for indels from annovar converted file.
I have already…
-
This rmsk annotation source is required by InterVar. However it seems no longer available ?
I tried to download with command:
`perl annotate_variation.pl --downdb --webfrom annovar -buildver hg19 …
-
4318样本的一个剪接位点,软件预测结果被覆盖。之前也出现过这个问题。
N004318 | 7 | 91737955 | 91737955 | G | C | splicing | AKAP9 | NM_147185:exon49:c.11662+8G>C;NM_005751:exon49:c.11686+8G>C | splicing SNV | . | - | NULL | NM_005…
-
Dear creators of nf-gwas-pipeline,
First a praise: I was looking for such a long time for a nice and well documented GWAS pipeline. I must say I've tried quite a few and there was always an issue so…
-
Hi,
I have a file with this format in bed with 689916 lines
#Chr Start End Ref Alt GIV_Indian_AAF
1 12673 12673 G A 0.001295
1 12719 12719 G …
-
Hi,
I am getting the following error when trying to run the example (with the following command: python3 Intervar.py -i example/ex1.avinput -o example/myanno). Would love any help in troubleshoot…
-
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…
-
Hello,
I try to run SNV-DA on my 40 samples, while the first 20 samples are in group 1 and the last 20 samples are in group 2. I created the variant files manually in the format requested.
I used thi…
-
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…