Celine Hoh

bcftools isec outputs all variants instead of just the common variants

1

Hi, I have two vcf files, `ALL.autosomes.phase3.vcf.gz` and `concat_ABCD_release_2.0.1_r1_filtered.vcf.gz`. `ALL.autosomes.phase3.vcf.gz` has 2504 subjects, while `concat_ABCD_release_2.0.1_r1_filtered.vcf.gz` has 10501 subjects. After doing `bcftools isec -c none -n=2 -p isec_ABCD_ref ALL.autosomes.phase3.vcf.gz concat_ABCD_release_2.0.1_r1_filtered.vcf.gz` to...

Empty Output File When Converting VCF to Haps

1

Hi! I am trying to convert my vcf files to hap, but I kept getting an empty output file. 1) My original vcf file looks like this, bcftools convert works...

Hi, I'm trying to liftover the CHESS_GRch38 annotation to CHM13 using this command `lifton -D -g /ccb/salz3/kh.chao/ref_genome/homo_sapiens/chess/chess3.0.1.gff_db -o /ccb/salz2/kh.chao/LiftOn/results/human_chess/lifton.gff3 --liftoff /ccb/salz2/kh.chao/LiftOn/results/human_chess/lifton_output/liftoff/liftoff.gff3_polished_db --miniprot /ccb/salz2/kh.chao/LiftOn/results/human_chess/lifton_output/miniprot/miniprot.gff3_db --proteins /ccb/salz2/kh.chao/LiftOn/results/human_chess/lifton_output/intermediate_files/proteins.fa --transcripts /ccb/salz2/kh.chao/LiftOn/results/human_chess/lifton_output/intermediate_files/transcripts.fa -polish -copies -sc...