Open niv280 opened 8 months ago
Hi niv280,
Can you share the shapeit5 command that you used, and the log file?
Thanks, Robin
Hi, I think that I understood what the problem. When I removed the ALT column from NON_REF to some kind of different ALT, it worked. So it's looks the the tool not supported in NON_REF, that make sense?
I also have the same problem. I am running the command:
phase_common --input output.vcf.gz --output allchr6.phased.vcf --thread 8 --region 6
and get the error:
[SHAPEIT5] phase_common (jointly phase multiple common markers)
- Author : Olivier DELANEAU, University of Lausanne
- Contact : olivier.delaneau@gmail.com
- Version : 5.1.1 / commit = f3ccf35 / release = 2024-02-27
- Run date : 07/03/2024 - 12:03:05
Files:
- Input : [output.vcf.gz]
- Output : [allchr6.phased.vcf]
- Output format : [bcf]
Parameters:
- Seed : 15052011
- Threads : 8 threads
- MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
- PBWT : [window = 4cM / depth = auto / modulo = auto / mac = 5 / missing = 0.1]
- HMM : [window = 4cM / Ne = 15000 / Constant recombination rate of 1cM per Mb]
Reading genotype data: [W::hts_idx_load3] The index file is older than the data file: output.vcf.gz.tbi
- VCF/BCF scanning done (0.01s)
- Variants [#sites=0 / region=6]
ERROR: No variants to be phased!
a snapshot from my VCF containing data from 130 individuals:
What may be the problem and how can I solve it?
Hi niv280,
Your ALT allele must be A,C,T or G for SNPs, or INDELS, but not "
Now I get a different error:
phase_common --input output.vcf.gz --output allchr6.phased.vcf --thread 8 --region chr6
[SHAPEIT5] phase_common (jointly phase multiple common markers)
- Author : Olivier DELANEAU, University of Lausanne
- Contact : olivier.delaneau@gmail.com
- Version : 5.1.1 / commit = f3ccf35 / release = 2024-02-27
- Run date : 07/03/2024 - 15:23:01
Files:
- Input : [output.vcf.gz]
- Output : [allchr6.phased.vcf]
- Output format : [bcf]
Parameters:
- Seed : 15052011
- Threads : 8 threads
- MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
- PBWT : [window = 4cM / depth = auto / modulo = auto / mac = 5 / missing = 0.1]
- HMM : [window = 4cM / Ne = 15000 / Constant recombination rate of 1cM per Mb]
Reading genotype data:
ERROR: AC field is needed in file
But my VCF do contain AC (I added it after getting this error message before, it can be seen in the previous screenshot)
Hi michal-yoles,
You also need to add the AN tag. AC and AN are used to compute allele frequency. You can easily fill those tags, eg. using bcftools +fill-AN-AC.
Cheers
It worked! Now I have a new error :)
I ran the command:
phase_common --input NA_AC_filteredChr6All.vcf.gz --pedigree All_CH_FA_MO.fam --output allch r6.phased.vcf --thread 8 --region chr6
and encountered the following error:
ERROR: Fail to index file [allchr6.phased.vcf]
What does it means? Although an output VCF is created, upon inspection, I notice cases of Mendel inconsistency. for example my fam file looks like this: the VCF contain a snp that looks like this:
chr6 398775 chr6_398775_G_A G A . . AC=32;AN=272 GT 0|1 0|1 0|1 0|1 0|0 1|0 0|0 0|1
where the two parents has haplotype of 0|0 and 1|0 (the sixth and the seventh) while the children has an haplotype of 0|1 which is not possible according to mendelian rules. Does it related to the error I encountered?
Hi, I'm trying to use phase_common_static to phase relative small VCF using ref_panel, and I'm getting the "No variant found" error I tried to compare my VCF and the ref panel and it seem there are at least 1 line in the same position that appear in both files.
Here is example for my vcf:
( I using fill tag to add AC before using phase_common)
Here is example for my ref_panel:
Any advise why there is no variant?