Comments (3)
ksamuk
commented on August 26, 2024
1
Hi Chen-Jui,
I'm not quite sure at the moment, that is going to be a complex fix to implement. In the meantime, a quick fix might be to preprocess your data using bcftools to set genotypes with DP < 1 to "." as below:
bcftools +setGT your.vcf.gz -- -t q -n . -e 'FMT/DP>=1'
Cheers,
Kieran
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ChenJuiYANG
commented on August 26, 2024
Hi Kieran,
I wonder what the result would be for the current version with the new GATK-generated vcf file as input. Does the results reliable?
Any suggestion if the new GATK-generated vcf file is not applicable?
Cheers,
Chen-Jui
from pixy.
ksamuk
commented on August 26, 2024
This is now addressed in the latest version of pixy.
from pixy.
Related Issues (20)
- Add support for arbitrary ploidy level (at least warn about incompatibility with polyploids) HOT 1
- RuntimeError: VCF file is missing mandatory header line ("#CHROM...") HOT 4
- pixy doesnt handle masked haplotype data?
- Using pixy without an all sites VCF? HOT 1
- Are these filter out sites not used in the calculation? HOT 1
- issues about multiple alleles and phasing sites
- bug
- 0 count of count_diffs and count_comparisons and all in count_missing HOT 11
- invariant vcf with ALT "*" instead of "." HOT 3
- - HOT 1
- <
- File corrupted HOT 1
- Calculate Missing data per window
- Pixy can't handle simple VCFs (PLINK output) HOT 2
- why can't I install pixy via conda? HOT 1
- 'DP' FORMAT header not found HOT 2
- version 1.2.11.beta1., pixy: error: unrecognized arguments: --variant_filter_expression DP -invariant_filter_expression DP
- All avg_dxy in pixy_dxy.txt is NA HOT 2
- can index big vcf
- About --chromosomes option
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