When I use a sorted bed file with unique 56,548 targets in it and process it in bedtools 2.25.0 with the below command:
I get 56,543 unique targets returned. The sort order is lexical in the bed and human in the bam so I use the -g option to specific the ordering of the bam. The 56,543 was confirmed in perl and awk. Any ideas why the two #'s are not the same? Thank you .
Code:
coverageBed -d -g /home/cmccabe/Desktop/NGS/bedtools2-25.0/genomes/human.hg19.Ion.genome.txt -a /home/cmccabe/Desktop/NGS/bed/bedtools/bedtools_unix_sorted_xgen_targets.bed -b /home/cmccabe/Desktop/NGS/IonXpress_004.R_2015_10_29_13_11_15_user_Proton-32-Lurie_Inh_Disease_151029_newheader.bam > /home/cmccabe/Desktop/NGS/IonXpress_004.R_2015_10_29_13_11_15_user_Proton-32-Lurie_Inh_Disease_151029_newheader_basecounts.bed
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