Comments (11)
Hi @shinlin77 ,
Thanks for your interest in VarCA! I've attached responses to each portion of your question below.
out/merged_snp/jurkat_chr1/final.tsv.gz
I think you're referring to the output of the prepare
subworkflow, which is not the final output of the entire pipeline. After the prepare
subworkflow, VarCA automatically runs the classify
subworkflow.
What is the final call? And is what should I use as the measure of confidence?
VCFs containing the final calls as well as QUAL scores with a measure of confidence for each call are generated at the end of the classify
subworkflow. That output is described here. Here's the path for the jurkat_chr1
sample:
out/classify/jurkat_chr1_snp/final.vcf.gz
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Thanks for getting back to me. That makes a lot more sense. One additional question, though. How are heterozygous calls designated? In the example, it seems like all the ALT are homozygous.
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The VCFs produced by VarCA lack the genotype (GT) field (see #11)
In theory, it should be possible to have 2vcf.py add that information to the VCFs, since I think most of the individual variant callers have it. But it might take a bit of a refactor, and I just haven't had the time to implement that.
Is that a feature that you'd like to have?
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That would be wonderful. The concept of your program should be useful for the community, but this feature would make it truly practical.
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ok, we'll see if I have some time for this
One caveat to this is that a variant may be incorrectly called homozygous (when, in fact, it's actually heterozygous) in situations where only one of the alleles has open chromatin
In other words, the GT info may be incorrect in loci with allele-specific open chromatin
Does that matter to you?
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you can quantify how often that happens, right?
In theory, it should be possible. In practice, it might be difficult. We could compare the scATAC-seq variants to variants from WGS, but there could be other reasons that the two would differ from each other besides allele-specific open chromatin. So we would have to come up with some measure (and a threshold on that measure) for detecting allele-specific open chromatin, and then filter for sites that pass the threshold.
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Hi @shinlin77 ,
I agree that it would be good to know. Somebody should do it. But developing a method to perform a test for allele specific chromatin is probably a whole project on its own. After all, testing for allele specific expression is kinda its own sub-field. I'm sorry, but I think that specific request is one that I do not personally have the bandwidth to implement within the foreseeable future.
But nonetheless, I'm going to keep this issue open to track progress on your request to add GT info to the VCFs. Afterwards, I will probably add a warning in the documentation explaining this situation and cautioning that the GT info may be inaccurate and should be ignored by the conventual user unless they have a way to account for allele specific open chromatin.
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(I'm just renaming the title of the issue to reflect its new purpose.)
If you have any other feature requests, kindly submit them in a new issue. Or, if you have a question or discussion item, you can add it to the Discussions tab.
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Related Issues (20)
- Classification model for mouse? HOT 2
- ChildIOException: File/directory is a child to another output: HOT 2
- Vardict error. HOT 1
- Varscan generates a REF allele that is not compatible with GATK. HOT 4
- 2vcf.py exits with a non-zero exit code when executed by snakemake HOT 3
- make channel specifications in environment files explicit
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- a smaller test dataset
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- Single-end support HOT 2
- Error: "An output file is marked as pipe, but consuming jobs are part of conflicting groups." HOT 11
- warn or error gracefully if index files don't exist
- Not all of the samples requested have provided input HOT 6
- handling a scATAC custom reference genome from 10x HOT 2
- VarDict-java produces malformed VCF HOT 5
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