# e.coli
/humgen/gsa-scr1/GATK_Data/Validation_Data/MV1994.bam         /humgen/gsa-scr1/GATK_Data/Validation_Data/Escherichia_coli_K12_MG1655.fasta      *

# daughter chrom 6 deep coverage first 10 MB
/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam  /broad/1KG/reference/human_b36_both.fasta   1:10,500,000-11,000,000

# daughter chrom 1 deep coverage
/broad/1KG/DCC/ftp/pilot_data/NA12878/alignment/NA12878.chrom1.SLX.SRP000032.2009_06.bam  /broad/1KG/reference/human_b36_both.fasta *

# mother of trio individual low coverage
/broad/1KG/DCC/ftp/pilot_data/NA12892/alignment/NA12892.SLX.SRP000031.2009_06.bam         /broad/1KG/reference/human_b36_both.fasta *

# Pilot 3
/broad/1KG/pilot3/sams/NA12892.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta *

# anthony PCR lane
# samtools import /seq/references/Homo_sapiens_assembly17/v0/Homo_sapiens_assembly17.bam.ref_list /seq/dirseq/aphilipp/combo/sequences/pcr/samfiles/10035.5.clean.sam 10035.5.clean.bam
/humgen/gsa-scr1/GATK_Data/Validation_Data/10035.5.clean.bam /humgen/gsa-scr1/GATK_Data/Validation_Data/Homo_sapiens_assembly17.fasta *

# anthony HS lane
# samtools import /seq/references/Homo_sapiens_assembly17/v0/Homo_sapiens_assembly17.bam.ref_list /seq/dirseq/aphilipp/combo/sequences/hs/samfiles/30CLA.5.clean.sam 30CLA.5.clean.bam
/humgen/gsa-scr1/GATK_Data/Validation_Data/30CLA.5.clean.bam /humgen/gsa-scr1/GATK_Data/Validation_Data/Homo_sapiens_assembly17.fasta *

# whole exom interval-based analysis for cancer
/humgen/gsa-scr1/GATK_Data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam         /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta      /humgen/gsa-scr1/GATK_Data/Validation_Data/TCGA-06-0188.interval_list

# WGS tumor -- figure it out
#/broad/1KG/pilot3/sams/NA12892.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta *

