mehrdadbakhtiari / adVNTR

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

http://advntr.readthedocs.io/

BSD 3-Clause "New" or "Revised" License

39 stars 15 forks source link

outformat #36

Closed psychrb closed 3 years ago

psychrb commented 3 years ago

For an adVNTR output in "vcf format:, is the command just --outfmt vcf I am getting bed and text to output, but not vcf...Not clear. If you can advise...Thanks. advntr genotype -m vntr_data/hg19_selected_VNTRs_Illumina.db -f BAM --working_directory ./ -of text -o NAME

Jong-hun-Park commented 3 years ago

Hi,

adVNTR supports VCF output since the version of 1.4.0. Can you first check if you used the right version? You can check the version from the output file or code (advntr/__init__.py).

The parameter --outfmt is the right way to specify the output format. It would be also helpful if you can let us know the exact command you used as I don't see the --outfmt parameter in the last line.

psychrb commented 3 years ago

The previous command had -of text parameter. Will check version.

psychrb commented 3 years ago

Yes, this did output a vcf file and version was the issue. The vcf seems transposed with rows instead of columns...Is that as per design...See below as header of vcf

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT

chr1
700243
.
CGAGGCGGGAAGATCACTTGATATCAGGAGTCGAGGCGGGAAGATCACTTGACGTCAGGAGTT .
.
.
END=700306;VID=156;RU=CGAGGCGGGAAGATCACTTGACATCAGGAGTT;RC=2 GT:DP:SR:FR:ML
0/0:34:13:21:1.0000 chr1
777293
.
AGAAATGCTTCTTTAGAAATGCTTCTTT
.
.
.
END=777321;VID=174;RU=AGAAATGCTTCTTT;RC=2
GT:DP:SR:FR:ML
0/0:37:20:17:1.0000

psychrb commented 3 years ago

Am I supposed to manually transpose the vcf output...? Or is this intended as adVNTR vcf output? Thanks.

Jong-hun-Park commented 3 years ago

Hi,

Thanks for checking the version. That's absolutely not intended behavior, and it is an issue caused by python version (That works with Python2). We will fix the issue very soon, but to use the fixed version, you will need to update the adVNTR using the latest code. How did you install adVNTR? through conda or github?

psychrb commented 3 years ago

Used Python 3 and current adVNTR version hosted on GitHub...Should Python 3 not be used then??

psychrb commented 3 years ago

I now see: 'Fix vcf output for both python2 and python3'. Should I re-load and run adVNTR again? With which Python version.

Jong-hun-Park commented 3 years ago

Yes, you need to re-load the code and re-install adVNTR again from Github. Sorry for the inconvenience. As of now, either Python 2 or 3 should work fine.