Open gustavahlberg opened 3 years ago
Hi Zheng Will you be addressing this anytime soon? Just need to know cause otherwise I will make a quick fix myself so I can move on.
Bw, Gustav
A quick fix could be:
f <- seqOpen("your_gds_file.gds", readonly=F)
node <- index.gdsn(f, "annotation/filter")
(s <- get.attr.gdsn(node)$Description)
put.attr.gdsn(node, "Description", unique(s))
seqClose(f)
Ah yes. Thank you!
In your case, did you merge multiple gds files with different variants? or multiple gds files with different samples?
different variants. Actually merging the 200K UKB exome vcfs (gds).
seqGDS2VCF is also printing "." filter as NA which cause some downstream error since NA is not declared in the header. And I don't know how to rewrite the header in the gds without messing something up. Also the contigs are converted to 'chrX' -> 'X' (which I prefer) but that is not changed in contigs listed in the header, which also cause some downstream errors. I tried to fix using write.gdsn() for "description/vcf.contig/ID" but it doesn't work.
Sorry, solved the last by just using add.gdsn instead of write.gdsn. And I added NA as a filterlevel in filter attribute which seem to work
"seqGDS2VCF is also printing "." filter as NA." It is fixed in the development version: http://www.bioconductor.org/packages/devel/bioc/news/SeqArray/NEWS
After having merged some gds files I am getting an error with seqGDS2VCF due to seqSummary() This stems from the .summary_filter() function were the attributes of the merged gds seems to somehow get twisted.
Filter attribute in one of the original gds files
Filter attribute in the merged gds