standardization not giving proper output

[Sendeman]

Running svtk standardize "(path to vcf)" "diploidSV(standardized).vcf" "manta"
creates a vcf output file with no variant calls.
The command is run in a server with a linux based terminal.

python version is 3.7.4

(changed filetype to .txt for upload)
diploidSV(standardized).vcf.txt

[biojiangke]

Any update with this issue? I'm having the same problem with empty variants (headers only VCF after standardization). My input VCF comes from Delly.

[ShirleyLiu-BCH]

same here

[SchKri]

I had the same issue. The problem was that by default GRCh37 contigs are used and my data was aligned to GRCh38. I used the --contigs option and it worked for me.

[biojiangke]

Using "--contigs" with the correct "fai" index file (the one used for original input VCF calling) did not work for me. But I'm working on a non-human organism.

[carolhuaxia]

I had the same issue. And I used the correct "fai" index file, get the output vcf only have the header with no variant records.

[carolhuaxia]

I had the same issue. And I used the correct "fai" index file, get the output vcf only have the header with no variant records.

I figure out the problem in my situation. The problem is caused by my sample ID which is digital. In the python script svtk/svtk/standardize/std_wham.py, there is a judgment in line 82 #if sample in raw_rec.info['TAGS']:#. If the sample ID is digital, the type of sample is int, while the content in raw_rec.info['TAGS'] is str. So the if is wrong.
I changed line82 to #if int(sample) in raw_rec.info['TAGS']:#, it solved my problem.