pslivar not working

[sitems]

I have small test vcf file with 6 variants. When running slivar, everything works as expected (shortened output):

$./slivar expr --js slivar-functions.js --vcf example.vcf.bgz --info "variant.FILTER == 'PASS'" | grep -v '^#' | wc -l [slivar] Finished. evaluated 6 total variants and wrote 6 variants that passed your slivar expressions. 6

But when I try pslivar, it is not working (shortened output):

$./pslivar expr --fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --js slivar-functions.js --vcf example.vcf.bgz --info "variant.FILTER == 'PASS'" | grep -v '^#' | wc -l [slivar] Finished. evaluated 0 total variants and wrote 0 variants that passed your slivar expressions. 0

fileformat=VCFv4.2

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CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Example

chr3 165504107 BCHE_acceptor_8bp_upstream A C 1000 . AC=2;AF=1 GT 1/1 chr1 16451824 EPHA2_cryptic_acceptor_9bp_upstream_exon17 C T 1000 . AC=2;AF=1 GT 1/1 chr9 136224694 SURF2_donor_4bp_downstream_exon3 A T 1000 . AC=2;AF=1 GT 1/1 chr12 6132066 VWF_acceptor_2bp_upstream_exon26_quid T C 1000 . AC=2;AF=1 GT 1/1 chr13 32930748 BRCA2_donor_2bp_downstream_exon15_quid T G 1000 . AC=2;AF=1 GT 1/1 chr2 47702319 MSH2_cryptic_donor C T 1000 . AC=2;AF=1 GT 1/1

[sitems]

I found the problem - different chromosome names between vcf and fasta.