Files and data associated with Khalfan et al., 2021 "Modifying Reference Sequence and Annotation Files Quickly and Reproducibly with *ref*orm" **The files are as follows:** Figure 2 files - **Mus_musculus.GRCm38_mb190.fa.gz:** reformed genome sequence - **Mus_musculus.GRCm38_mb190.gff3:** reformed genome annotation - **mb190.bam:** alignment on unreformed genome - **mb190_reform.bam:** alignment using reformed genome - **mb190_indels_gatk.vcf:** indels on unreformed genome alignments - **mb190_indels_reform_gatk.vcf:** indels using reformed genome alignments - **mb190_snps_gatk.vcf:** snps on unreformed genome alignments - **mb190_snps_reform_gatk.vcf:** snps using reformed genome alignments Figure 3 files - **Saccharomyces_cerevisiae_DGY1910.fa:** reformed genome sequence - **Saccharomyces_cervisiae_DGY1910.gff:** reformed gff - **DGY22203_sniffles.vcf:** variants calls on unreformed genome alignments - **DGY2203_reform_sniffles.vcf:** variant calls using reformed genome ---------- **The data for Figure 2 was generated as follows:** BAM and VCF files generated using https://github.com/gencorefacility/variant-calling-pipeline. Number of reads in BAM obtained using samtools: `samtools view mb190.bam 6:52257694-52260880 | wc -l` (6:52257694-52260880 are the coordinates of the HOXA13 gene) Number of variants in VCF obtained using tabix: `bgzip mb190_snps_gatk.vcf` `tabix -p vcf mb190_snps_gatk.vcf.gz` `tabix -R hoxa13-region.txt mb190_snps_gatk.vcf.gz | wc -l` `