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file_paths.py
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file_paths.py
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# Full depth mt grch38
pilot_grch38 = 'gs://neurogap/high_coverage/NeuroGap_30x_Pilot_Callset.mt'
# Gencove mt hg19
gencove_0.5_hg19 = 'gs://neurogap/high_coverage/gencove/merge_0.5_hg19.mt'
gencove_1_hg19 = 'gs://neurogap/high_coverage/gencove/merge_1_hg19.mt'
gencove_2_hg19 = 'gs://neurogap/high_coverage/gencove/merge_2_hg19.mt'
gencove_4_hg19 = 'gs://neurogap/high_coverage/gencove/merge_4_hg19.mt'
gencove_6_hg19 = 'gs://neurogap/high_coverage/gencove/merge_6_hg19.mt'
# Gencove mt grch38
gencove_0.5_grch38 = 'gs://neurogap/high_coverage/gencove/merge_0.5_grch38.mt'
gencove_1_grch38 = 'gs://neurogap/high_coverage/gencove/merge_1_grch38.mt'
gencove_2_grch38 = 'gs://neurogap/high_coverage/gencove/merge_2_grch38.mt'
gencove_4_grch38 = 'gs://neurogap/high_coverage/gencove/merge_4_grch38.mt'
gencove_6_grch38 = 'gs://neurogap/high_coverage/gencove/merge_6_grch38.mt'
gencove_metadata = 'gs://neurogap/high_coverage/gencove/fastq_keep.txt'
# Beagle imputed mt
beagle_0.5_imputed = 'gs://neurogap/high_coverage/neurogap_0.5X.imputed.mt'
beagle_1_imputed = 'gs://neurogap/high_coverage/neurogap_1.0X.imputed.mt'
beagle_2_imputed = 'gs://neurogap/high_coverage/neurogap_2.0X.imputed.mt'
beagle_4_imputed = 'gs://neurogap/high_coverage/neurogap_4.0X.imputed.mt'
beagle_6_imputed = 'gs://neurogap/high_coverage/neurogap_6.0X.imputed.mt'
# Beagle refined mt
beagle_0.5_refined = 'gs://neurogap/high_coverage/neurogap_0.5X.refined.mt'
beagle_1_refined = 'gs://neurogap/high_coverage/neurogap_1.0X.refined.mt'
beagle_2_refined = 'gs://neurogap/high_coverage/neurogap_2.0X.refined.mt'
beagle_4_refined = 'gs://neurogap/high_coverage/neurogap_4.0X.refined.mt'
beagle_6_refined = 'gs://neurogap/high_coverage/neurogap_6.0X.refined.mt'
# Raw calls
beagle_0.5_raw = 'gs://neurogap/high_coverage/neurogap_0.5X.mt'
beagle_1_raw = 'gs://neurogap/high_coverage/neurogap_1.0X.mt'
beagle_2_raw = 'gs://neurogap/high_coverage/neurogap_2.0X.mt'
beagle_4_raw = 'gs://neurogap/high_coverage/neurogap_4.0X.mt'
beagle_6_raw = 'gs://neurogap/high_coverage/neurogap_6.0X.mt'
# Bam file list
bam_files = '/Users/alicia/daly_lab/neurogap/data/high_coverage/bam_files.txt'
# Full coverage meta-data
# Sample ID and site map
sample_id_map = 'gs://neurogap/high_coverage/sample_id_map.txt'
# Depth
full_depth = 'gs://neurogap/high_coverage/WGS/downsample-bam.txt'