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somatic_variant_calling_get_reads_1.sh
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somatic_variant_calling_get_reads_1.sh
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#!/bin/bash
# ------------------- Download reads ------------------- #
# N-D (Normal Duodenal tissue)
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/NYGC_Illumina-WGS_20231023/HG008-N-D_CGGACAAC-AATCCGGA_H3LLJDSXC_L001_001.R1.fastq.gz ../reads/
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/NYGC_Illumina-WGS_20231023/HG008-N-D_CGGACAAC-AATCCGGA_H3LLJDSXC_L001_001.R2.fastq.gz ../reads/
# T (Pancreatic Ductal Adenocarcinoma Cell Line (PDAC))
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/NYGC_Illumina-WGS_20231023/HG008-T_TTCCTGTT-AAGATACT_HJVY2DSX7_L001_001.R1.fastq.gz ../reads/
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/NYGC_Illumina-WGS_20231023/HG008-T_TTCCTGTT-AAGATACT_HJVY2DSX7_L001_001.R2.fastq.gz ../reads/
# ------------------- Subset reads ------------------- #
# subsetting 1,000,000 reads from each fastq
cd ../reads/
seqtk sample -s100 HG008-N-D_CGGACAAC-AATCCGGA_H3LLJDSXC_L001_001.R1.fastq.gz 1000000 > HG008-N-D_CGGACAAC-AATCCGGA_subset_H3LLJDSXC_L001_001.R1.fastq
seqtk sample -s100 HG008-N-D_CGGACAAC-AATCCGGA_H3LLJDSXC_L001_001.R2.fastq.gz 1000000 > HG008-N-D_CGGACAAC-AATCCGGA_subset_H3LLJDSXC_L001_001.R2.fastq
seqtk sample -s100 HG008-T_TTCCTGTT-AAGATACT_HJVY2DSX7_L001_001.R1.fastq.gz 1000000 > HG008-T_TTCCTGTT-AAGATACT_subset_HJVY2DSX7_L001_001.R1.fastq
seqtk sample -s100 HG008-T_TTCCTGTT-AAGATACT_HJVY2DSX7_L001_001.R2.fastq.gz 1000000 > HG008-T_TTCCTGTT-AAGATACT_subset_HJVY2DSX7_L001_001.R2.fastq