Comments (4)
from truvari.
candidateSV.vcf.gz
Hello, thank you for answering as I have checked the .vcf file earlier it has no FORMAT & SAMPLE column present and I read some earlier issues from truvari git and added FORMAT(GT) & SAMPLE(.) in my vcf files manually but I suppose the files aren't compatible with truvari when I add these columns manually.
from truvari.
There must have been an error in how the format and sample was added. I ran the following script and was able to run on its output VCF.
- fixer.py:
import sys
for line in sys.stdin:
if line.startswith("##"):
sys.stdout.write(line)
elif line.startswith("#"):
sys.stdout.write('##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n')
sys.stdout.write(line.strip() + '\tFORMAT\tSAMPLE\n')
else:
sys.stdout.write(line.strip() + '\tGT\t.\n')
- command line
gunzip -c candidateSV.vcf.gz| python fixer.py | bgzip > cand_fix.vcf.gz
from truvari.
Thank you so much finally it's working for me now.
from truvari.
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