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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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limit to only autosomes #170

Closed prasundutta87 closed 1 month ago

prasundutta87 commented 1 month ago

Hi @brentp ,

I am trying to get some de novo SVs for some genes with biallelic mode of inheritance. I am using this command-

slivar expr --vcf autosomal_recessive_SVs/"$family"_panel_genes_SVs.vcf --trio "biallelic_denovo:(variant.CHROM != \"chrX\"||variant.CHROM != \"chrY\") && (kid.het||kid.hom_alt) && mom.hom_ref && dad.hom_ref && kid.DP >= 5 && mom.DP >= 5 && dad.DP >= 5 && (mom.DV + dad.DV) == 0" --ped $PED_FILE_PATH/"$family".ped --pass-only -o biallelic_de_novo_SVs/"$family"_de_novo_SVs_in_biallelic_genes.vcf

However, I am still getting X chrosome SV VCF records. What might be the issue here? Is there a better way to limit myself only to autosomes for this?

Regards, Prasun

brentp commented 1 month ago

hi, is it "chrX" or just "X" ?

brentp commented 1 month ago

instead of:

(variant.CHROM != \"chrX\"||variant.CHROM != \"chrY\")

you likely want:

(variant.CHROM != \"chrX\" && variant.CHROM != \"chrY\")

and note that you can use single quotes to simplify:

(variant.CHROM != 'chrX' && variant.CHROM != 'chrY')
prasundutta87 commented 1 month ago

Hi @brentp .. thanks a lot for this. It has worked now.