Comments (5)
Hi @tytrhr,
Thanks for your question. You are correct. STAARpipeline takes genotype data by chromosome to analyze large sequencing data, and thus you may split VCF files by chromosome before VCF2GDS processing.
Best,
Xihao
from staarpipeline-tutorial.
Thanks for your reply, I found a script that can implement this step, “Rscript convertVCF2GDS.R import.format vcf base.filename 2 chr22.vcf.gz chr2.vcf.gz”, I would like to ask if this command setting is correct? In addition, the vcf file is split, so does this step require a single processing? I find that when I run this scripts, the results are merged together, only base.filename.gds. Looking forward to your reply, thank you very much!
from staarpipeline-tutorial.
Hi @tytrhr, do you have all VCF files split by each chromosome already?
from staarpipeline-tutorial.
Hi, xihao, yes, I have. Thank you very much for your reply! In addition, I would like to ask, how does the linux system correctly download the FAVORannotator's database? I find the FAVORannotator's database on the https://favor.genohub.org, such as "chr1 CSV (31.2 GB) Download", right click on the "Download" to copy address, use wget to download, but the file is 6170506 and can not be used; directly click "Download" and then upload the linux system, the file is chr1.tar.gz and can be used correctly. I don't know what causes this, can you give me some suggestions?
from staarpipeline-tutorial.
Hi @tytrhr,
Thanks for letting me know. Both ways would result in the same correct file. If you are using wget
for download, please feel free to follow this R script for the next step of FAVORannotator.
Best,
Xihao
from staarpipeline-tutorial.
Related Issues (20)
- fit_nullmodel Output is mostly Null and 0 HOT 16
- Fitting NULL model for binary outcomes HOT 5
- Error in Gene Centric Analysis HOT 1
- Error in results_plof_genome[, "cMAC"] : subscript out of bounds HOT 2
- Followup Question to Issue #28 HOT 2
- STAARpipeline_Gene_Centric_Noncoding HOT 2
- Dynamic Window dim(X) error HOT 3
- Can't annotate individual variant results HOT 2
- [Suggestion-Implementation] Add information to summary and annotations of results HOT 1
- Conditional analysis - Summary Gene Centric Noncoding not running to completion HOT 6
- Ukbiobank Agds files generation HOT 16
- Plots for gene centric ncRNA regions HOT 5
- FATAL ERROR - Too many first alleles as the major allele (~21.5%). HOT 1
- warning messages in generating the annotated GDS (aGDS) file. HOT 3
- Controls / cases counts inverted when using binary model HOT 7
- kinship matrix HOT 2
- variant set in gene-centric coding/noncoding analysis HOT 2
- in the Step 2: Individual (single-variant) analysis, Error in if (chr == 1) { : argument is of length zero HOT 3
- Error : Mat::operator(): index out of bounds & Error in apply(emthr_SCANG_O, 2, max) : HOT 1
- What is the difference between the "results_temp" and "results_m" results? HOT 1
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