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createPHG.md

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Connect to compute machines

salloc module load miniconda source activate my-phg conda activate phgv2-conda

Preprocessing data

phg prepare-assemblies --keyfile phg-wheat/keyfile --output-dir phg-wheat/updated_assemblies --threads 5

Build VCF data

sbatch phg-wheat/script.sh phg create-ranges --reference-file phg-wheat/updated_assemblies/iwgsc_refseqv2.1_assembly_short.fa --gff phg-wheat/updated_assemblies/Triticum_aestivum_refseqv2.IWGSC_RefSeq_v2.1.58.chr.gff3 --boundary gene --pad 500 --range-min-size 500 -o phg-wheat/bed/file.bed