Closed psychrb closed 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.
The previous command had -of text parameter. Will check version.
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
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
Am I supposed to manually transpose the vcf output...? Or is this intended as adVNTR vcf output? Thanks.
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?
Used Python 3 and current adVNTR version hosted on GitHub...Should Python 3 not be used then??
I now see: 'Fix vcf output for both python2 and python3'. Should I re-load and run adVNTR again? With which Python version.
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.
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