Comments (1)
This error occurs whenever pysam (a wrapper around htslib) encounters a monomorphic reference variant call and there is an attempt to access ALT records. You can filter these sites and create a new input for truvari with the commands:
bcftools view -c 1 input.vcf -O z -o new_file.vcf.gz
tabix new_file.vcf.gz
See 31e4a49
from truvari.
Related Issues (20)
- Clarification of the output (fp.vcf) and the FP field in the summary.txt HOT 2
- Clarification needed over the summary.txt file HOT 3
- Reindexing only valid with uniquely valued Index objects HOT 2
- vcf2df in help message for segment
- ‘truvari collapse -k maxqual‘ does not work for me HOT 4
- Invalid argument and BCF warning HOT 2
- KeyError: 'invalid FORMAT: GT' during truvari bench HOT 1
- Effects of case on indel comparison HOT 1
- Conda installation -- issue with header definitions when running truvari HOT 4
- No TP-base and TP-call match in the benchmark results HOT 3
- Question about logging in collapse HOT 2
- A quick query about correlation HOT 1
- Please update collapse wiki HOT 1
- Truvari bench finds no calls in vcf file. HOT 5
- query about VCF bed intersection HOT 2
- error from collapse function : TypeError: invalid value for Integer format HOT 2
- Can't install via conda or pip HOT 2
- Error with Truvari collapse from bcftools-merged Manta VCFs HOT 1
- --choose behavior HOT 5
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from truvari.