Comments (5)
this is now in master and i'll make a new release shortly
you can do, e.g.
export SOMALIER_ALLOWED_FILTERS=LowGQX,NoPassedVariantGTs
somalier extract ...
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Relatedly, is there a description of the minimum requirements for a variant to be extracted? All I could find was the AD check defaulting to GT if AD isn't available.
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i will document the requirements. briefly it requires the FILTER is one of "PASS", "", ".", "RefCall"
then, when genotyping, it uses allele-balance AB. with HOM-REF < 0.04, HOM-ALT > 0.96, HET 0.2 to 0.8 and all else is unknown.
what is the FILTER of the variants you'd like to include? I'd rather add more things like "RefCall" than add extra flags.
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To be honest, it's a lot of weird filters that shouldn't pass under normal conditions (things like LowGQX;NoPassedVariantGTs
), but due to the way this test captures the sequencing it throws off the filters even when the variant call is good.
Sounds like my best path forward would be to just pre-parse the gVCFs such that somalier will accept the variants (i.e. reduce it down to PASS
and a GT
field only).
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I'll make this an environment variable, something like SOMALIER_ALLOWED_FILTERS in a future release, for now, yes, you can use some simple awk to pre-process.
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Related Issues (20)
- convert somalier format to VCF/PED HOT 2
- Relate Killed? HOT 4
- No pedigree inference in samples from same family HOT 1
- bam files without `@RG` tag HOT 4
- Sex QC for one sample HOT 7
- Legend results in relatedness plot HOT 2
- [Question]: difference between sites.hg38.vcf.gz and sites.hg38.rna.vcf.gz HOT 2
- Re-use of inferred parent names in large families HOT 1
- SIGSEGV: Illegal storage access. (Attempt to read from nil?) HOT 2
- Failing to run find-sites HOT 10
- sex check HOT 6
- How sex is inferred HOT 1
- Why this is a male? HOT 1
- Relatedness color pattern issue in plot HOT 6
- IBS1 count
- Extracted genotypes format? HOT 2
- Inference questions
- sm1.somalier and no other output HOT 5
- [error] SIGSEGV: Illegal storage access. (Attempt to read from nil?) Segmentation fault (core dumped) ( HOT 14
- Scaled mean depth on X - how to calculate? HOT 1
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