Examples of comp-het for duo, solo and also small variants with CNV

[qwzhang0601]

Hi Brentp:

Thanks for the great tool. We are trying to call comound-het with slivar. We have tested with trios following your examples below. I wonder whether you have some example scripts for duo and solo some where? We tried to created some JS functions to cover trio, duo, solo, but run into some error when we test with slivar.

Besides, we also want to include different variant types, e.g., SNP and CNV. I do see some description, but wonder there are some existing scripts we can follow.

#the examples for trio we found
https://github.com/brentp/slivar/blob/master/paper/slivar.nf

Thanks

Best
Quanwei

[qwzhang0601]

Hi Brentp:

If you could kindly take a look. We have prepared the attached JS file, and tested with the following script and get some error like this "[slivar] javascript error. this can some times happen when a field is missing.
error from duktape: ReferenceError: identifier 's' undefined for expression:comphet_side_auto(s)"

#script for the test
#!/bin/bash

in_vcf=example_trio.vep.vcf
in_ped=example_trio_pedgree.ped
in_gnomad=gnomad.hg38.genomes.v3.fix.zip
out_vcf=./test_result/slivar_annotated.vcf

slivar expr
--vcf $in_vcf
--ped $in_ped
--gnotate $in_gnomad
--js js/slivar-comphet-functions.js
--out-vcf $out_vcf
--info "INFO.impactful && INFO.gnomad_popmax_af < 0.01 && INFO.gnomad_nhomalt < 5"
--family-expr 'comphet_side:comphet_side_auto(s)'

#compound het
comp_het_vcf=slivar_annotated_comp_het.vcf

/mnt/pure3/bioinfo/qzhang/tools/slivar/slivar compound-hets -v $out_vcf
--sample-field comphet_side -p $in_ped > $comp_het_vcf

#tsv
comp_het_tsv=slivar_annotated_comp_het.tsv

slivar tsv
-s slivar_comphet
-i gnomad_popmax_af -i gnomad_popmax_af_filter -i gnomad_nhomalt
-c CSQ
--csq-column ALLELE
-p $in_ped
$comp_het_vcf > $comp_het_tsv

slivar-comphet-functions.js

Thanks

Best
Quanwei