[cmccabe]

Yes the output makes more sense now thank you . I indexed the bam in samtools but didn't sort it as it appears it already was. Out of curiosity

cmccabe@DTV-A5211QLM:~/Desktop/NGS$ samtools view -H /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902.bam | head -10
@HD	VN:1.4	GO:none	SO:coordinate
@SQ	SN:chr1	LN:249250621
@SQ	SN:chr2	LN:243199373
@SQ	SN:chr3	LN:198022430
@SQ	SN:chr4	LN:191154276
@SQ	SN:chr5	LN:180915260
@SQ	SN:chr6	LN:171115067
@SQ	SN:chr7	LN:159138663
@SQ	SN:chr8	LN:146364022
@SQ	SN:chr9	LN:141213431

cmccabe@DTV-A5211QLM:~/Desktop/NGS$ coverageBed -d -sorted -a /home/cmccabe/Desktop/NGS/bed/sorted_unix_5column_xgen_targets.bed -b /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902.bam > /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_counts.txt
ERROR: [B]chromomsome sort ordering for file /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902.bam is inconsistent with other files. Record was:[/B]
chr10	68734	68755	X28LU:04418:11727	6	+

Output (674 MB)

chr1	955542	955763	+	AGRN:exon.1	1	0
chr1	955542	955763	+	AGRN:exon.1	2	0
chr1	955542	955763	+	AGRN:exon.1	3	0
chr1	955542	955763	+	AGRN:exon.1	4	1
chr1	955542	955763	+	AGRN:exon.1	5	1
chr1	955542	955763	+	AGRN:exon.1	6	1
chr1	955542	955763	+	AGRN:exon.1	7	1

I can not find that record in the bam file, is that a sequencing error, a bug, or something unique to Ion Torrent bam files? Thank you .