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===BAC Data=== The BAC data is on genome miner, in the following path: */media/LTS_33T/KZ_LTS33T/PGP1_BacPool The folder contains several subfolders: *old_calls **Contains the old variant call files *vcf_files **Contains a lot of vcf files *all_pools_combined **Contains all the heterozygous call files. Still unsure of the format *fixed.bam **Contains all of the bam files for each index *filtered_vcf **Seems to contain the newest .vcf files, probably the best ones to use *assembled_haplotypes **Contains the final phase output of HapCUT that was used for the BAC pools *het_sites **Contains the heterozygous site files for each chromosome. Still unsure of the format
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