7. Read Processing & Mapping

We trim and map all samples using PaleoMix--v1.2.5. For the GBS samples, we used the same .yaml file used above, the only difference being that now we used the filtered .fastq files.

GBS Samples (¡PCR duplicates ARE NOT removed here!):

xsbatch -c XXX --mem-per-cpu XXX -J GBS --time XXX -- bam_pipeline run --jre-option "-XmxXXXg" --max-threads XXX --bwa-max-threads XXX --adapterremoval-max-threads XXX --destination ~/data/Pigeons/PBGP/Analyses/PaleoMix_GBS/ ~/data/Pigeons/PBGP/PBGP--Analyses/PBGP--Final_PaleoMix_GBS.yaml

WGS Samples (¡PCR duplicates ARE removed here!):

xsbatch -c XXX --mem-per-cpu XXX -J Re-Seq --time XXX -- bam_pipeline run --jre-option "-XmxXXXg" --max-threads XXX --bwa-max-threads XXX --adapterremoval-max-threads XXX --destination ~/data/Pigeons/Analysis/PaleoMix_Re-Sequencing/ ~/data/Pigeons/Analysis/FPGP--Final_PaleoMix_Re-Sequencing.yaml

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