Codes_used.txt

#All 1000G files can be acquired from here: http://ftp.1000genomes.ebi.ac.uk/vol1/

wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree;	#GIVES THE LIST OF ALL FILES AVAILABLE IN 1000G RELEASE 3#
grep -hnr '.bam' current.tree > All_BAMfiles.list;		#ONLY KEEP THE LINES THAT HAS .bam#
sed -i '/.bam.bai/d' All_BAMfiles.list;				#REMOVE THE .bam.bai FILES#
sed -i '/.bam.bas/d' All_BAMfiles.list;				#REMOVE THE .bam.bas FILES#
sed -i '/cram/d' All_BAMfiles.list;				#REMOVE THE .cram FILES#
sed -i '/chrom/d' All_BAMfiles.list;				#REMOVE THE Chromosome specific  FILES#
sed -i '/exome/d' All_BAMfiles.list;				#REMOVE THE exome sequencing FILES#
sed -i '/unmapped/d' All_BAMfiles.list;				#REMOVE THE UNMAPPED FILES#
sed -i '/csra/d' All_BAMfiles.list;				#REMOVE THE .csra FILES#
sed -i '/technical/d' All_BAMfiles.list;			#REMOVE THE 'technical' FILES#
awk '/CEU/' All_BAMfiles.list > test;				#KEEP ONLY CENTRAL EUROPEAN ANCESTRY SPECIFIC FILES#
awk '!_[$1]++' test > All_BAMfiles.list;			#REMOVE ALL DUPLICATES#
awk '/bwa/' All_BAMfiles.list > test && mv test All_BAMfiles.list;	#KEEP ONLY 'bwa' string matched files#
sed -i '/evidence/d' All_BAMfiles.list;				#REMOVE ALL EVIDENCE SPECIFIC OR SUPPORT FILES#
grep '.bam' All_BAMfiles.list | cut -f 1 | sed 's/.*://g' > test && mv test All_BAMfiles.list;	 #KEEP ONLY THE FTP LINK OF THE SELECTED BAM FILES#

#TO GET COVERAGE (around chrmosome 1, base pair 40000 to 50000) FROM ALL THESE SAMPLE BAM FILES#

cat All_BAMfiles.list | while read line; do samtools depth -r 1:40000-50000 "http://ftp.1000genomes.ebi.ac.uk/vol1/$line" && rm -f *.bam.bai; done &> Chr01_4000_to_5000.txt

#THIS WILL SAVE THE RESULTS IN THE FILE NAMED Chr01_4000_to_5000.txt#

#The options used for samtools execution can be found here: http://www.htslib.org/doc/samtools.html

#-----------------------------------------------------------------------------------------------------------------------------------------------
#NOT RUN#
#The example I created can be generated like this:
#The example_BAMfiles.list only includes three individuals, hence it suns faster. The actual result will include 183 individuals.
#cat Example_BAMfiles.list | while read line; do samtools depth -r 1:40000-40005 "http://ftp.1000genomes.ebi.ac.uk/vol1/$line" && rm -f *.bam.bai; done &> Example_output_Chr01_40000_to_40005.txt

#---------------------------------------------------------METOD-2-------------------------------------------------------------------------------
#WHAT TO DO#
#CREATE ANE FILE WITH 'TAB' DELIMITION THAT INCLUDES ALL THE SNPS IN THE FOLLOWING STRUCTURE:#
#1	123456	 123456# #SNP IN CHROMOSOME 1 WITH BASEPAIR POSITION 123456#
#8	234567	 234567# #SNP IN CHROMOSOME 8 WITH BASEPAIR POSITION 234567#
#FOR AN EXAMPLE SEE: Sample_SNPfile.bed#
#REMEMBER!! THE EXTENSION OF THE SNP FILE NEEDS TO BE '.bed'#

#THEN RUN THE FOLLOWING:#

cat All_BAMfiles.list | while read line; do samtools depth -b MY_SNP_FILE.bed "http://ftp.1000genomes.ebi.ac.uk/vol1/$line" && rm -f *.bam.bai; done &> OUTPUT_I_WANT.txt;

#-----------------------------------------------------------------------------------------------------------------------------------------------
#NOT RUN#
#The example I created can be generated like this:
#The example_BAMfiles.list only includes three individuals, hence it suns faster. The actual result will include 183 individuals.
#The example SNP file only includes two SNPs for demonstration.
#THE ACTUAL PROGRAM WILL RUN FOR A REALLY LONG TIME#
#cat Example_BAMfiles.list | while read line; do samtools depth -b Sample_SNPfile.bed "http://ftp.1000genomes.ebi.ac.uk/vol1/$line" && rm -f *.bam.bai; done &> Example_output.txt;

#---------------------------------------------------------------METHOD-3-------------------------------------------------------------------------
#SCRATCH THAT, I HAVE FOUND MORE EFFICIENT WAY TO DO THIS#
#CREATE A FILE WITH DESCRIPTION OF ALL SNPs IN THE FOLLOWING STRUCTURE:#
#1#	#SNP IN CHROMOSOME 1 WITH BASEPAIR POSITION 40000#
#40000#
#2#	#SNP IN CHROMOSOME 2 WITH BASEPAIR POSITION 50000#
#50000#
#FOR AN EXAMPLE SEE: Sample_SNPfile_r.txt#
#REMEMBER!! TO KEEP JUST ONE EMPTY LINE AT THE END OF THE FILE#

#CHANGE THE FILENAMES TO INCLUDE ALL SNPs AND ALL SAMPLES IN THE SCRIPT FILE: 'Extract_Depth_All_SNP.sh'#
#THEN RUN THE FOLLOWING:#

./Extract_Depth_All_SNP.sh

#THIS WILL CREATE N NUMBER OF FILES. N IS NUMBER OF TOTAL SNPS. EACH FILE WILL INCLUDE DEPTH CALCULATED FOR EACH INDIVIDUAL IN 1000G IN EACH LINE#

#-----------------------------------------------------------------------------------------------------------------------------------------------
#NOT RUN#
#The example I created can be generated like this:
#The example_BAMfiles.list only includes three individuals, hence it suns faster. The actual result will include 183 individuals.
#The example SNP file only includes two SNPs for demonstration.
#THE ACTUAL PROGRAM WILL RUN FOR A REALLY LONG TIME#
#./Extract_Depth_All_SNP.sh #OFCOURSE RUN THIS BEFORE CHANGING ANYTHING INSIDE THE FILE#