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I am using:
The newheader.bam is sorted like so:
Since the bam file is uses "human ordering, I sorted the bed file in the same way using the -faidx option in bedtools.
The output file that results stops after chr19. I guess my question is if there was an error sorting wouldn't all the records be a problem and if I made my own genome file using the coordinates in the bedtools genome file but re-ordered them to match mine, would that work? Or is there another problem I am overlooking? Thank you 
.
Edit: I just needed a customized genome file and that solved it. Thank you.
Code:
cmccabe@DTV-A5211QLM:~/Desktop/NGS$ coverageBed -d -sorted -g /home/cmccabe/Desktop/NGS/bedtools2-25.0/genomes/human.hg19.genome -a /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets_sorted.bed -b /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_newheader.bam > /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_output.txt [B]Error: Sorted input specified, but the file /home/cmccabe/Desktop/NGS/bed/bedtools/xgen_targets_sorted.bed has the following record with a different sort order than the genomeFile /home/cmccabe/Desktop/NGS/bedtools2-25.0/genomes/human.hg19.genome chr20 126045 126343 + DEFB126:exon.2;DEFB126:exon.3[/B]
Code:
cmccabe@DTV-A5211QLM:~/Desktop/NGS/pool_I_090215$ samtools view -H IonXpress_008_150902_newheader.bam | grep SQ | cut -f 2 | awk '{ sub(/^SN:/, ""); print;}'
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
chrM
Code:
cmccabe@DTV-A5211QLM:~/Desktop/NGS/bed/bedtools$ awk '!_[$1]++' | cut -f1 xgen_targets_sorted.bed | uniq chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY
.Edit: I just needed a customized genome file and that solved it. Thank you
.