HPRC2 MC panel (with variants > 25kb away from large bubbles removed)

HPRC2 panel with samples HG00733 and NA19240, as well as all variants > 25kb away from SV bubbles removed. Steps to regenerate: zcat mc_filtered_ids.vcf.gz | python3 create-bed.py > svs_25kb.bed bedtools merge -i svs_25kb.bed > svs_25kb_merged.bed bcftools view -s ^HG00733,NA19240 mc_filtered_ids.vcf.gz | bcftools view --min-ac 1 -Oz -o mc_filtered_ids_only-samples.vcf.gz tabix -p vcf mc_filtered_ids_only-samples.vcf.gz bedtools intersect -a mc_filtered_ids_only-samples.vcf.gz -b svs_25kb_merged.bed -wa -u -sorted -header | bgzip > mc_filtered_ids_only-samples_25kb.vcf.gz tabix -p vcf mc_filtered_ids_only-samples_25kb.vcf.gz bcftools view --trim-alt-alleles mc_filtered_ids_only-samples_25kb.vcf.gz -Oz -o mc_filtered_ids_only-samples_25kb_trimmed.vcf.gz tabix -p vcf mc_filtered_ids_only-samples_25kb_trimmed.vcf.gz