vcf to gds

[wangshuang2024]

Hello, @xihaoli.
In the script of "Varinfo_gds.R" and "gds2agds.R", it has two gds name.
gds_file_name_1 <- "freeze.5.chr"
gds_file_name_2 <- ".pass_and_fail.gtonly.minDP0.gds"

I wonder what the two documents represent and how they are produced? Thank you.

[xihaoli]

Hi @wangshuang2024,

Thanks for reaching out. The gds_file_name_1 and gds_file_name_2 are both part of the target gds file name, separated by the chr number. For example, if the target gds file is for chromosome 1, and

gds_file_name_1 <- "freeze.5.chr"
gds_file_name_2 <- ".pass_and_fail.gtonly.minDP0.gds"

then after string concatenation, the target GDS file should have name freeze.5.chr1.pass_and_fail.gtonly.minDP0.gds.

Hope this helps.

Best,
Xihao

[wangshuang2024]

Hi @wangshuang2024,

Thanks for reaching out. The gds_file_name_1 and gds_file_name_2 are both part of the target gds file name, separated by the chr number. For example, if the target gds file is for chromosome 1, and

gds_file_name_1 <- "freeze.5.chr"
gds_file_name_2 <- ".pass_and_fail.gtonly.minDP0.gds"

then after string concatenation, the target GDS file should have name freeze.5.chr1.pass_and_fail.gtonly.minDP0.gds.

Hope this helps.

Best, Xihao

Thank you , I got it.

[wangshuang2024]

Hello, @xihaoli . I got another problem and hope you can help me.
In step 2 Annotate the variants.
for i in 'seq 1 22'; do Rscript /Rscript/staarpipeline/Annotate.R ${i}; done
After I run this code. I got an error.

Warning message:
NAs introduced by coercion
Error in 1:chr_splitnum : NA/NaN argument
Execution halted

How can I solve this? Thank you for your help.

[xihaoli]

Hi @wangshuang2024,

It seems like your chr_splitnum in line 33 of Annotate.R is NA. Can you make sure whether the path of your file_DBsplit is set correctly? You may perform a manual check by setting chr <- 1 in line 24 of Annotate.R).

Thanks,
Xihao

[wangshuang2024]

Hi @wangshuang2024,

It seems like your chr_splitnum in line 33 of Annotate.R is NA. Can you make sure whether the path of your file_DBsplit is set correctly? You may perform a manual check by setting chr <- 1 in line 24 of Annotate.R).

Thanks, Xihao

Thank you, @xihaoli . I figure out this problem. There is another error.

     used (Mb) gc trigger (Mb) max used (Mb)

Ncells 269061 14.4 654582 35 444042 23.8
Vcells 448538 3.5 8388608 64 1771786 13.6
[1] 1
No such file or directory (os error 2)
[1] 2
No such file or directory (os error 2)
[1] 3
No such file or directory (os error 2)
Selector index 1 is out of bounds. Index must be >= 1 and <= 0.

I check the path of "file_DBsplit","DB_path“，”xsv” and "output_path", they are all correct.

DB name like this "/reference/FAVOR/essentialDB/chr1.tar.gz"

[xihaoli]

Hi @wangshuang2024,

You would need to first uncompress the chr1.tar.gz file before running Annotate.R.

Best,
Xihao

[wangshuang2024]

Hi @wangshuang2024,

You would need to first uncompress the chr1.tar.gz file before running Annotate.R.

Best, Xihao

Thank you, Xihao. I solve these problems.