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=BAC Data Processing= [[Daniel:Notebook/Haplotyping|Back to Notebook]] This page describes the data processing for the BAC data in the haplotyping project. For data locations, visit the [https://docs.google.com/spreadsheets/d/1gStTrST8MaWWlHeXMeWXVpjsNvRn8HUdeC4gSUbnPxQ/edit#gid=1124859722 Data Map]. ==Processing== #samtools targetcut ##Uses read depth from the data to assign reads into contigs ##[[Media:Targetcut.txt|Script]] #Split the BAC Contigs by chromosome ##HAPCUT reads the data by chromosome, so the fragments need to be split up by chromosome; they also must remain split by index ##[[Media:Bam_2_bam.sh|Script]] #Extract HAIRS ##HAPCUT program to extract haplotype informative reads (HAIRS) from each chromosome; extracted by index/chromosome then merged by chromosome ##[[Media:Extracthairs_bychrom.sh|Script]]
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