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Old 09-29-2015, 02:46 PM   #1
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 349
Default coverageBed -g option error

I am using:

Code:
[email protected]:~/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
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
The newheader.bam is sorted like so:

Code:
[email protected]:~/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
Since the bam file is uses "human ordering, I sorted the bed file in the same way using the -faidx option in bedtools.

Code:
[email protected]:~/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
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 .

Last edited by cmccabe; 09-30-2015 at 05:23 PM. Reason: solved
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