Comments (4)
Hello,
In theory I don't see a reason why it wouldn't work, however, it is not been benchmarked at all for this use case. There may be parameters that need to be tweaked, and other technical confounders that need to be considered (e.g. off-target DNA contamination). Sorry that I can't provide more guidance than that.
- Stephane
from phaser.
Thanks for your reply, and what you're thinking about is exactly what I'm worried about. Now i attempt to deal with some ChIp-seq data, but you know the depth of these samples is generally not enough to search for ASB by using heterozygous loci .So i want to try haplotype. Unfortunately i don't know the parental genotypes of experimental individuals. Can you give me some advices for this problem?
Thank you!
from phaser.
Assuming these are humans, I would phase the VCF using a population based reference panel (e.g. 1000 Genomes, HRC, etc...), for example with https://imputationserver.sph.umich.edu/. Then use the phased VCF as input for phASER.
from phaser.
Thanks for your advice. I'll try it.
from phaser.
Related Issues (20)
- FATAL ERROR: No heterozygous sites that passed all filters were included in the analysis HOT 19
- phaser_gene_ae output with 0 Count? HOT 1
- Retrieve parent of origin for haplotypes HOT 1
- Advice on how to run phASER with RNA-seq data only and posed genotypes of parents HOT 1
- what kind of vcf file i can use?
- phASER error
- question regarding input vcf HOT 4
- Error running phaser HOT 3
- version of phaser on github
- Issues with phaser-pop HOT 2
- Container HOT 3
- phaser.py requires pysam HOT 1
- trying to locate phASER_GTEx_v8_merged.vcf.gz for phaser_cis_var.py (phaser-pop)
- Error in using phaser_gene_ae.py HOT 6
- parameter '--no_gw_phase 0' HOT 2
- phaser annotate module is still py2.7? HOT 3
- Recommendations for running phaser with just the rnaseq data HOT 3
- phaser_cis_var.py HOT 1
- Issue in function split_read
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