Tabix issue :The regions are not sorted ,Could not read

Question

[arya.sagittarius]

Step 1 : I had converted a bedfile from hg19 -->hg38 using crossmap.py.

Step2: Sorted it BEDTools/bin/sortBed -i Hg19_to_Hg38.bed> Hg19_to_Hg38_sorted.bed

Step3: Doing tabix /htslib/tabix -h -R Hg19_to_Hg38_sorted.bed gnomad.genomes.v3.1.2.hgdp_tgp.chrY.vcf. bgz > ChrY.vcf

The regions are not sorted: chr1:120888022-120889411 is before chr1:120888022-120888079 Could not read Hg19_to_Hg38_sorted.bed

I am facing this error while running, but there is no position as chr1:120888022-120889411 in the bed file and also I have checked this Hg19_to_Hg38_sorted.bed and its sorted. why is my file not being read ?

[Pierre Lindenbaum]

that is not the syntax I would use (and t's not clear why your mixing vcf and bed in your commands...)

sort -t $'\t' -k1,1 -k2,2n Hg19_to_Hg38.bed | bgzip > Hg19_to_Hg38_sorted.bed.gz
tabix -p bed Hg19_to_Hg38_sorted.bed.gz

[arya.sagittarius]

I wanted to extract the regions in the bed from the genome file

[Pierre Lindenbaum]

what is "the genome file" ???

[arya.sagittarius]

gnomad v3 genome files

[arya.sagittarius]

this worked. thank you so much